AnalysisController Object
(
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    [uses] => Array
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            [1] => AnnotSource
            [2] => Configuration
            [3] => Similarities
            [4] => GeneFamily
            [5] => GeneFamilyTypes
            [6] => Msa
            [7] => GfDatum
            [8] => AdExperiments
            [9] => FunctionalClustersExperiments
            [10] => Trees
        )

    [helpers] => Array
        (
            [Session] => 
            [Html] => 
            [Form] => 
            [Cache] => 
        )

    [components] => Array
        (
            [Session] => 
            [DataUtils] => 
            [FunctionalAnnotationUtils] => 
            [GeneFamilies] => 
            [Organism] => 
            [Blast] => 
            [WorkbenchUtils] => 
            [PhylogeneticModuleUtils] => 
            [ExternalPrograms] => 
            [FastaUtils] => 
            [MsaUtils] => 
            [PhylogeneticUtils] => 
            [Sequence] => 
            [RequestHandler] => 
        )

    [request] => CakeRequest Object
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                (
                    [plugin] => 
                    [controller] => analysis
                    [action] => custom_tree_creation
                    [named] => Array
                        (
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                    [pass] => Array
                        (
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                    [isAjax] => 
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            [data] => Array
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            [query] => Array
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            [webroot] => /plaza.dev/_dev_instances/feedback/
            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
            [_detectors:protected] => Array
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                    [get] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => GET
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                    [patch] => Array
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                            [env] => REQUEST_METHOD
                            [value] => PATCH
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                    [post] => Array
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                            [env] => REQUEST_METHOD
                            [value] => POST
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                    [put] => Array
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                            [env] => REQUEST_METHOD
                            [value] => PUT
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                    [delete] => Array
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                            [env] => REQUEST_METHOD
                            [value] => DELETE
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                    [head] => Array
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                            [env] => REQUEST_METHOD
                            [value] => HEAD
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                    [options] => Array
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                            [env] => REQUEST_METHOD
                            [value] => OPTIONS
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                    [ssl] => Array
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                            [env] => HTTPS
                            [value] => 1
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                    [ajax] => Array
                        (
                            [env] => HTTP_X_REQUESTED_WITH
                            [value] => XMLHttpRequest
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                    [flash] => Array
                        (
                            [env] => HTTP_USER_AGENT
                            [pattern] => /^(Shockwave|Adobe) Flash/
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                    [mobile] => Array
                        (
                            [env] => HTTP_USER_AGENT
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                                    [1] => AvantGo
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                                    [10] => MIDP
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                                    [13] => Opera Mini
                                    [14] => Opera Mobi
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                                    [16] => PalmSource
                                    [17] => portalmmm
                                    [18] => Plucker
                                    [19] => ReqwirelessWeb
                                    [20] => SonyEricsson
                                    [21] => Symbian
                                    [22] => UP\.Browser
                                    [23] => webOS
                                    [24] => Windows CE
                                    [25] => Windows Phone OS
                                    [26] => Xiino
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                        )

                    [requested] => Array
                        (
                            [param] => requested
                            [value] => 1
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                    [json] => Array
                        (
                            [accept] => Array
                                (
                                    [0] => application/json
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                            [param] => ext
                            [value] => json
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                    [xml] => Array
                        (
                            [accept] => Array
                                (
                                    [0] => application/xml
                                    [1] => text/xml
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                            [param] => ext
                            [value] => xml
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                )

            [_input:protected] => 
        )

    [response] => CakeResponse Object
        (
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                    [101] => Switching Protocols
                    [200] => OK
                    [201] => Created
                    [202] => Accepted
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                    [301] => Moved Permanently
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                    [303] => See Other
                    [304] => Not Modified
                    [305] => Use Proxy
                    [307] => Temporary Redirect
                    [400] => Bad Request
                    [401] => Unauthorized
                    [402] => Payment Required
                    [403] => Forbidden
                    [404] => Not Found
                    [405] => Method Not Allowed
                    [406] => Not Acceptable
                    [407] => Proxy Authentication Required
                    [408] => Request Time-out
                    [409] => Conflict
                    [410] => Gone
                    [411] => Length Required
                    [412] => Precondition Failed
                    [413] => Request Entity Too Large
                    [414] => Request-URI Too Large
                    [415] => Unsupported Media Type
                    [416] => Requested range not satisfiable
                    [417] => Expectation Failed
                    [429] => Too Many Requests
                    [500] => Internal Server Error
                    [501] => Not Implemented
                    [502] => Bad Gateway
                    [503] => Service Unavailable
                    [504] => Gateway Time-out
                    [505] => Unsupported Version
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            [_mimeTypes:protected] => Array
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                    [html] => Array
                        (
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                            [1] => */*
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                    [json] => application/json
                    [xml] => Array
                        (
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                            [1] => text/xml
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                            [1] => application/vnd.ms-excel
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                    [dcr] => application/x-director
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                    [f4v] => video/mp4
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                    [f4b] => audio/mp4
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                    [jpeg] => image/jpeg
                    [jpe] => image/jpeg
                    [pbm] => image/x-portable-bitmap
                    [pgm] => image/x-portable-graymap
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                    [wrl] => model/vrml
                    [mime] => www/mime
                    [pdb] => chemical/x-pdb
                    [xyz] => chemical/x-pdb
                    [javascript] => application/javascript
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                    [file] => multipart/form-data
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                            [1] => application/xhtml
                            [2] => text/xhtml
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                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
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            [_protocol:protected] => HTTP/1.1
            [_status:protected] => 200
            [_contentType:protected] => text/html
            [_headers:protected] => Array
                (
                )

            [_body:protected] => 
            [_file:protected] => 
            [_fileRange:protected] => 
            [_charset:protected] => UTF-8
            [_cacheDirectives:protected] => Array
                (
                )

            [_cookies:protected] => Array
                (
                )

        )

    [_responseClass:protected] => CakeResponse
    [viewPath] => Analysis
    [layoutPath] => 
    [viewVars] => Array
        (
            [sidebar] => gene_sidebar
            [navigation_bar_info] => Array
                (
                    [num_colinearity_runs] => 1
                    [num_colinearity_with_dating_runs] => 0
                    [num_functional_clusters_runs] => 6
                    [has_pan_genomes] => 
                    [has_blast_db] => 1
                )

            [allowed_extra_sequences_types] => Array
                (
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                    [dna] => DNA
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            [allowed_editing_methods] => Array
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                    [row] => Genes only
                    [column_row] => Positions and Genes
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            [allowed_tree_programs] => Array
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            [allowed_msa_programs] => Array
                (
                    [muscle] => MUSCLE
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            [allowed_number_blasthits] => Array
                (
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                    [1] => 20
                    [2] => 10
                    [3] => 5
                    [4] => 1
                )

            [similarity_hits_genes] => Array
                (
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                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.87PAU8
                            [e_value] => 1.4e-182
                            [bit_score] => 642.9
                            [alignment_length] => 343
                            [identity_percentage] => 100.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.GW23Z6] => Array
                        (
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                            [e_value] => 1.3e-132
                            [bit_score] => 476.9
                            [alignment_length] => 370
                            [identity_percentage] => 75.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.T41GG2] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.T41GG2
                            [e_value] => 1.7e-127
                            [bit_score] => 459.9
                            [alignment_length] => 316
                            [identity_percentage] => 75.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.625I4R] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.625I4R
                            [e_value] => 6.4e-127
                            [bit_score] => 458.0
                            [alignment_length] => 373
                            [identity_percentage] => 67.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.LDA4IK] => Array
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                            [e_value] => 3.2e-126
                            [bit_score] => 455.7
                            [alignment_length] => 316
                            [identity_percentage] => 75.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.3AR30J] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.3AR30J
                            [e_value] => 4.2e-126
                            [bit_score] => 455.3
                            [alignment_length] => 316
                            [identity_percentage] => 75.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
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                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.ZY293U] => Array
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                            [e_value] => 7.1e-126
                            [bit_score] => 454.5
                            [alignment_length] => 316
                            [identity_percentage] => 75.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.9T44NN] => Array
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                            [gene_id] => arahy.Tifrunner.gnm1.ann1.9T44NN
                            [e_value] => 9.3e-126
                            [bit_score] => 454.1
                            [alignment_length] => 316
                            [identity_percentage] => 75.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.JB5G6S] => Array
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                            [gene_id] => arahy.Tifrunner.gnm1.ann1.JB5G6S
                            [e_value] => 9.3e-126
                            [bit_score] => 454.1
                            [alignment_length] => 316
                            [identity_percentage] => 74.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.4R1N6H] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.4R1N6H
                            [e_value] => 1.2e-125
                            [bit_score] => 453.8
                            [alignment_length] => 316
                            [identity_percentage] => 74.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.7UIB1D] => Array
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                            [gene_id] => arahy.Tifrunner.gnm1.ann1.7UIB1D
                            [e_value] => 2.1e-125
                            [bit_score] => 453.0
                            [alignment_length] => 316
                            [identity_percentage] => 74.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.390B12] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.390B12
                            [e_value] => 1.3e-124
                            [bit_score] => 450.3
                            [alignment_length] => 316
                            [identity_percentage] => 74.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.HIWB5S] => Array
                        (
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                            [bit_score] => 450.3
                            [alignment_length] => 316
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                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.86RVGQ] => Array
                        (
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                            [bit_score] => 449.5
                            [alignment_length] => 316
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.HQL5ZH] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.HQL5ZH
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                            [bit_score] => 449.5
                            [alignment_length] => 316
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.44H41D] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.44H41D
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                            [bit_score] => 448.7
                            [alignment_length] => 316
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.NZ73MH] => Array
                        (
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                            [bit_score] => 448.7
                            [alignment_length] => 316
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.PTE4RY] => Array
                        (
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                            [bit_score] => 448.4
                            [alignment_length] => 316
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.TLT0RJ] => Array
                        (
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                            [bit_score] => 448.4
                            [alignment_length] => 313
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.19B2C5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.19B2C5
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                            [bit_score] => 448.0
                            [alignment_length] => 308
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.DX7X9L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.DX7X9L
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                            [bit_score] => 446.8
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.VG5MUL] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.VG5MUL
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                            [bit_score] => 446.8
                            [alignment_length] => 370
                            [identity_percentage] => 65.9
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.YKB7VN] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.YKB7VN
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                            [bit_score] => 446.4
                            [alignment_length] => 308
                            [identity_percentage] => 76.0
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.K985UN] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.K985UN
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                            [bit_score] => 446.0
                            [alignment_length] => 308
                            [identity_percentage] => 76.0
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.T3114H] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.T3114H
                            [e_value] => 2.5e-123
                            [bit_score] => 446.0
                            [alignment_length] => 370
                            [identity_percentage] => 67.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.0FE5EB] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.0FE5EB
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                            [bit_score] => 445.3
                            [alignment_length] => 308
                            [identity_percentage] => 75.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.22A0BZ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.22A0BZ
                            [e_value] => 4.3e-123
                            [bit_score] => 445.3
                            [alignment_length] => 308
                            [identity_percentage] => 74.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.G16GBW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.G16GBW
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                            [bit_score] => 445.3
                            [alignment_length] => 308
                            [identity_percentage] => 75.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.DILN7M] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.DILN7M
                            [e_value] => 5.6e-123
                            [bit_score] => 444.9
                            [alignment_length] => 308
                            [identity_percentage] => 75.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.MF1Z11] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.MF1Z11
                            [e_value] => 5.6e-123
                            [bit_score] => 444.9
                            [alignment_length] => 308
                            [identity_percentage] => 75.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.N38U72] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.N38U72
                            [e_value] => 7.4e-123
                            [bit_score] => 444.5
                            [alignment_length] => 377
                            [identity_percentage] => 66.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.67AQV3] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.67AQV3
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                            [bit_score] => 443.7
                            [alignment_length] => 308
                            [identity_percentage] => 75.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.EDB0QK] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.EDB0QK
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                            [bit_score] => 443.7
                            [alignment_length] => 308
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.HWFE7W] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.HWFE7W
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                            [bit_score] => 443.7
                            [alignment_length] => 308
                            [identity_percentage] => 75.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.8U8QG7] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.8U8QG7
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                            [alignment_length] => 316
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.PC9UR1] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.PC9UR1
                            [e_value] => 1.6e-122
                            [bit_score] => 443.4
                            [alignment_length] => 308
                            [identity_percentage] => 75.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.618FAS] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.618FAS
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                            [bit_score] => 443.0
                            [alignment_length] => 308
                            [identity_percentage] => 75.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D001651
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                    [arahy.Tifrunner.gnm1.ann1.Y4MBR7] => Array
                        (
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                            [bit_score] => 442.2
                            [alignment_length] => 308
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.KB372Z] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.KB372Z
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                            [bit_score] => 441.0
                            [alignment_length] => 308
                            [identity_percentage] => 75.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.X8XTSC] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.X8XTSC
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                            [bit_score] => 441.0
                            [alignment_length] => 316
                            [identity_percentage] => 73.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.ZU9EK6] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ZU9EK6
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                            [bit_score] => 441.0
                            [alignment_length] => 308
                            [identity_percentage] => 74.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.G6BTHS] => Array
                        (
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                            [bit_score] => 440.7
                            [alignment_length] => 308
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.XF3T5B] => Array
                        (
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                            [bit_score] => 440.7
                            [alignment_length] => 308
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.JSYE9A] => Array
                        (
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                            [bit_score] => 440.3
                            [alignment_length] => 308
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.L849KL] => Array
                        (
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                            [bit_score] => 439.9
                            [alignment_length] => 308
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.LIE4DR] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.LIE4DR
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                            [alignment_length] => 308
                            [identity_percentage] => 74.4
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.5U1Y5S] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.5U1Y5S
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                            [bit_score] => 439.5
                            [alignment_length] => 307
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.BCFP52] => Array
                        (
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                            [bit_score] => 439.1
                            [alignment_length] => 304
                            [identity_percentage] => 75.0
                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.AX1X9T] => Array
                        (
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                            [bit_score] => 438.7
                            [alignment_length] => 316
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.F7WSSH] => Array
                        (
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                            [bit_score] => 437.2
                            [alignment_length] => 308
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.P91A7Q] => Array
                        (
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                            [bit_score] => 436.8
                            [alignment_length] => 317
                            [identity_percentage] => 72.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.3DW5CS] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.3DW5CS
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                            [bit_score] => 436.0
                            [alignment_length] => 308
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.P60MR3] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.P60MR3
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                            [bit_score] => 436.0
                            [alignment_length] => 308
                            [identity_percentage] => 74.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Q47VXP] => Array
                        (
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                                (
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                        (
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                            [alignment_length] => 304
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                                (
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                        (
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                            [alignment_length] => 308
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D001651
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                        (
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                            [alignment_length] => 308
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 304
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                                (
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                        (
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ICE72P
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                            [alignment_length] => 316
                            [identity_percentage] => 72.8
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M3XE2W
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                            [bit_score] => 430.3
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.YH0HYY
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                            [bit_score] => 428.3
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.3413VH
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                            [alignment_length] => 316
                            [identity_percentage] => 71.8
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.PDU7VZ
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                            [bit_score] => 425.6
                            [alignment_length] => 316
                            [identity_percentage] => 73.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.Y3RU0I] => Array
                        (
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                            [bit_score] => 424.9
                            [alignment_length] => 316
                            [identity_percentage] => 71.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.X7WWLG] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.X7WWLG
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                            [bit_score] => 424.1
                            [alignment_length] => 300
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.D3KQFI] => Array
                        (
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                            [bit_score] => 422.9
                            [alignment_length] => 338
                            [identity_percentage] => 69.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.UN49J0] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.UN49J0
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                            [bit_score] => 422.2
                            [alignment_length] => 316
                            [identity_percentage] => 76.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.79H2ZA] => Array
                        (
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                            [bit_score] => 418.7
                            [alignment_length] => 302
                            [identity_percentage] => 71.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.M915JV] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M915JV
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                            [bit_score] => 417.5
                            [alignment_length] => 292
                            [identity_percentage] => 80.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.IUFC7V] => Array
                        (
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                            [bit_score] => 413.7
                            [alignment_length] => 366
                            [identity_percentage] => 62.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.3TU4M5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.3TU4M5
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                            [bit_score] => 411.4
                            [alignment_length] => 297
                            [identity_percentage] => 72.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.7580UM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.7580UM
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                            [bit_score] => 407.9
                            [alignment_length] => 285
                            [identity_percentage] => 75.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.UCKJ4P] => Array
                        (
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                            [bit_score] => 406.8
                            [alignment_length] => 292
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.BW0SGT] => Array
                        (
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                            [bit_score] => 403.7
                            [alignment_length] => 308
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.U0J92L] => Array
                        (
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                            [bit_score] => 398.7
                            [alignment_length] => 296
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.0I80A4] => Array
                        (
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                            [bit_score] => 396.4
                            [alignment_length] => 268
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.5KY2TX] => Array
                        (
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                            [bit_score] => 389.0
                            [alignment_length] => 294
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.ITS72S] => Array
                        (
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                            [bit_score] => 387.5
                            [alignment_length] => 366
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.HM98QR] => Array
                        (
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                            [bit_score] => 385.6
                            [alignment_length] => 343
                            [identity_percentage] => 64.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.NVTW2S] => Array
                        (
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                            [bit_score] => 384.8
                            [alignment_length] => 280
                            [identity_percentage] => 72.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.P2IVNE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.P2IVNE
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                            [bit_score] => 382.9
                            [alignment_length] => 314
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [bit_score] => 381.3
                            [alignment_length] => 289
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.WU79S3] => Array
                        (
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                            [bit_score] => 380.9
                            [alignment_length] => 292
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.K76VAT] => Array
                        (
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                            [bit_score] => 378.6
                            [alignment_length] => 362
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.LT085V] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.LT085V
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                            [bit_score] => 378.6
                            [alignment_length] => 306
                            [identity_percentage] => 67.3
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                        (
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                            [bit_score] => 375.9
                            [alignment_length] => 272
                            [identity_percentage] => 74.3
                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.RVWB0M] => Array
                        (
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                            [bit_score] => 372.5
                            [alignment_length] => 272
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.FG7H5S] => Array
                        (
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                            [bit_score] => 370.2
                            [alignment_length] => 308
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                        (
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                            [bit_score] => 370.2
                            [alignment_length] => 308
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.MI8TNQ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.MI8TNQ
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                            [bit_score] => 367.1
                            [alignment_length] => 321
                            [identity_percentage] => 66.0
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                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.CQ5GAN] => Array
                        (
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                            [e_value] => 9.7e-99
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                            [alignment_length] => 340
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                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 289
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                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 281
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [bit_score] => 355.5
                            [alignment_length] => 265
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.YM3WRX] => Array
                        (
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                            [alignment_length] => 313
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                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.AXU1GU] => Array
                        (
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                            [alignment_length] => 261
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 316
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                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 350
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                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [bit_score] => 324.3
                            [alignment_length] => 264
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.Q9UUMB] => Array
                        (
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                            [bit_score] => 322.8
                            [alignment_length] => 241
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.217P67] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.217P67
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                            [bit_score] => 314.7
                            [alignment_length] => 248
                            [identity_percentage] => 69.0
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.SPE56M] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.SPE56M
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                            [bit_score] => 312.4
                            [alignment_length] => 247
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.YRHH3L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.YRHH3L
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                            [alignment_length] => 269
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.IE1D11] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IE1D11
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                            [alignment_length] => 276
                            [identity_percentage] => 66.7
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.6U6G8M] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.6U6G8M
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                            [bit_score] => 308.1
                            [alignment_length] => 312
                            [identity_percentage] => 57.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.C593YE] => Array
                        (
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                            [alignment_length] => 269
                            [identity_percentage] => 62.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.31ESZ9] => Array
                        (
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                            [bit_score] => 306.6
                            [alignment_length] => 269
                            [identity_percentage] => 62.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.UQ4A0Q] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.UQ4A0Q
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                            [bit_score] => 305.4
                            [alignment_length] => 235
                            [identity_percentage] => 71.1
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.FHGQ5B] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.FHGQ5B
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                            [bit_score] => 302.4
                            [alignment_length] => 205
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.AR04AZ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.AR04AZ
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                            [bit_score] => 301.6
                            [alignment_length] => 255
                            [identity_percentage] => 65.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.6I2GPK] => Array
                        (
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                            [alignment_length] => 288
                            [identity_percentage] => 59.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 301
                            [identity_percentage] => 61.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.2708NW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.2708NW
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                            [bit_score] => 298.9
                            [alignment_length] => 201
                            [identity_percentage] => 76.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.35BD43] => Array
                        (
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                            [bit_score] => 296.2
                            [alignment_length] => 227
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 198
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.XJX9BL] => Array
                        (
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.62B9ZV] => Array
                        (
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                            [bit_score] => 295.8
                            [alignment_length] => 277
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [bit_score] => 294.7
                            [alignment_length] => 340
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.UNC6RI] => Array
                        (
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                            [bit_score] => 294.7
                            [alignment_length] => 198
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.EXLZ0E] => Array
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [bit_score] => 291.2
                            [alignment_length] => 260
                            [identity_percentage] => 68.8
                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.AQ8SFL] => Array
                        (
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                            [bit_score] => 286.2
                            [alignment_length] => 187
                            [identity_percentage] => 77.5
                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 248
                            [identity_percentage] => 66.5
                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                        (
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                            [alignment_length] => 198
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.EA1KS6] => Array
                        (
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                            [bit_score] => 283.1
                            [alignment_length] => 177
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                            [bit_score] => 279.6
                            [alignment_length] => 177
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                            [species] => arhy
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.1H3RP1] => Array
                        (
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                            [bit_score] => 275.0
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                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.QV8Q6T] => Array
                        (
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                            [bit_score] => 274.2
                            [alignment_length] => 228
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.SSLH32] => Array
                        (
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                            [bit_score] => 273.5
                            [alignment_length] => 268
                            [identity_percentage] => 61.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.Y0F1XT] => Array
                        (
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                            [bit_score] => 266.2
                            [alignment_length] => 259
                            [identity_percentage] => 67.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.4GS65V] => Array
                        (
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                            [bit_score] => 262.7
                            [alignment_length] => 197
                            [identity_percentage] => 72.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.D940DF] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.D940DF
                            [e_value] => 8.8e-68
                            [bit_score] => 261.5
                            [alignment_length] => 177
                            [identity_percentage] => 75.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.FK4Q8T] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.FK4Q8T
                            [e_value] => 2.6e-67
                            [bit_score] => 260.0
                            [alignment_length] => 177
                            [identity_percentage] => 76.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.4TEP00] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.4TEP00
                            [e_value] => 2.2e-66
                            [bit_score] => 256.9
                            [alignment_length] => 316
                            [identity_percentage] => 51.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.ZD1FV2] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ZD1FV2
                            [e_value] => 2.2e-66
                            [bit_score] => 256.9
                            [alignment_length] => 219
                            [identity_percentage] => 65.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.I0MGU7] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.I0MGU7
                            [e_value] => 4.8e-66
                            [bit_score] => 255.8
                            [alignment_length] => 184
                            [identity_percentage] => 73.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.RTS1QS] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.RTS1QS
                            [e_value] => 4.8e-66
                            [bit_score] => 255.8
                            [alignment_length] => 164
                            [identity_percentage] => 77.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.96FB1P] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.96FB1P
                            [e_value] => 1.4e-65
                            [bit_score] => 254.2
                            [alignment_length] => 198
                            [identity_percentage] => 70.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.D12JGJ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.D12JGJ
                            [e_value] => 2.4e-65
                            [bit_score] => 253.4
                            [alignment_length] => 197
                            [identity_percentage] => 68.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.I4SF0Q] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.I4SF0Q
                            [e_value] => 2.4e-65
                            [bit_score] => 253.4
                            [alignment_length] => 164
                            [identity_percentage] => 77.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Z0B08L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Z0B08L
                            [e_value] => 5.0e-63
                            [bit_score] => 245.7
                            [alignment_length] => 167
                            [identity_percentage] => 76.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.VE75MW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.VE75MW
                            [e_value] => 4.2e-62
                            [bit_score] => 242.7
                            [alignment_length] => 245
                            [identity_percentage] => 53.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Q6JBKT] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Q6JBKT
                            [e_value] => 9.5e-62
                            [bit_score] => 241.5
                            [alignment_length] => 178
                            [identity_percentage] => 67.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.J30PZF] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.J30PZF
                            [e_value] => 4.7e-61
                            [bit_score] => 239.2
                            [alignment_length] => 148
                            [identity_percentage] => 78.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.35SW51] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.35SW51
                            [e_value] => 6.1e-61
                            [bit_score] => 238.8
                            [alignment_length] => 167
                            [identity_percentage] => 75.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.FC8ITA] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.FC8ITA
                            [e_value] => 8.0e-61
                            [bit_score] => 238.4
                            [alignment_length] => 174
                            [identity_percentage] => 72.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.9VH52Z] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.9VH52Z
                            [e_value] => 4.9e-58
                            [bit_score] => 229.2
                            [alignment_length] => 124
                            [identity_percentage] => 87.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.CDRG1U] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.CDRG1U
                            [e_value] => 4.9e-58
                            [bit_score] => 229.2
                            [alignment_length] => 124
                            [identity_percentage] => 87.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.15G177300] => Array
                        (
                            [gene_id] => Glyma.15G177300
                            [e_value] => 6.3e-58
                            [bit_score] => 228.8
                            [alignment_length] => 312
                            [identity_percentage] => 42.3
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Q7RZT9] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Q7RZT9
                            [e_value] => 1.1e-57
                            [bit_score] => 228.0
                            [alignment_length] => 254
                            [identity_percentage] => 49.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.X2BPFT] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.X2BPFT
                            [e_value] => 3.2e-57
                            [bit_score] => 226.5
                            [alignment_length] => 155
                            [identity_percentage] => 76.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.YN5V9H] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.YN5V9H
                            [e_value] => 3.2e-57
                            [bit_score] => 226.5
                            [alignment_length] => 284
                            [identity_percentage] => 45.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.B2TA0B] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.B2TA0B
                            [e_value] => 5.4e-57
                            [bit_score] => 225.7
                            [alignment_length] => 265
                            [identity_percentage] => 49.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.20G037200] => Array
                        (
                            [gene_id] => Glyma.20G037200
                            [e_value] => 7.0e-57
                            [bit_score] => 225.3
                            [alignment_length] => 313
                            [identity_percentage] => 42.5
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.89MAKE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.89MAKE
                            [e_value] => 1.2e-56
                            [bit_score] => 224.6
                            [alignment_length] => 153
                            [identity_percentage] => 77.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.19G068000] => Array
                        (
                            [gene_id] => Glyma.19G068000
                            [e_value] => 2.7e-56
                            [bit_score] => 223.4
                            [alignment_length] => 312
                            [identity_percentage] => 41.7
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.20G060800] => Array
                        (
                            [gene_id] => Glyma.20G060800
                            [e_value] => 2.7e-56
                            [bit_score] => 223.4
                            [alignment_length] => 316
                            [identity_percentage] => 41.1
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Z01BNV] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Z01BNV
                            [e_value] => 3.5e-56
                            [bit_score] => 223.0
                            [alignment_length] => 210
                            [identity_percentage] => 65.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.DWAY4T] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.DWAY4T
                            [e_value] => 1.0e-55
                            [bit_score] => 221.5
                            [alignment_length] => 179
                            [identity_percentage] => 69.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.15G210800] => Array
                        (
                            [gene_id] => Glyma.15G210800
                            [e_value] => 2.3e-55
                            [bit_score] => 220.3
                            [alignment_length] => 314
                            [identity_percentage] => 41.4
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.RC9HZP] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.RC9HZP
                            [e_value] => 2.9e-55
                            [bit_score] => 219.9
                            [alignment_length] => 275
                            [identity_percentage] => 46.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.N3KJBP] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.N3KJBP
                            [e_value] => 8.6e-55
                            [bit_score] => 218.4
                            [alignment_length] => 115
                            [identity_percentage] => 90.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.FFB5CH] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.FFB5CH
                            [e_value] => 1.9e-54
                            [bit_score] => 217.2
                            [alignment_length] => 146
                            [identity_percentage] => 75.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.18G122400] => Array
                        (
                            [gene_id] => Glyma.18G122400
                            [e_value] => 9.5e-54
                            [bit_score] => 214.9
                            [alignment_length] => 303
                            [identity_percentage] => 41.6
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.18G150700] => Array
                        (
                            [gene_id] => Glyma.18G150700
                            [e_value] => 2.1e-53
                            [bit_score] => 213.8
                            [alignment_length] => 304
                            [identity_percentage] => 42.1
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.03G079900] => Array
                        (
                            [gene_id] => Glyma.03G079900
                            [e_value] => 3.6e-53
                            [bit_score] => 213.0
                            [alignment_length] => 313
                            [identity_percentage] => 39.6
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.219KTT] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.219KTT
                            [e_value] => 1.4e-52
                            [bit_score] => 211.1
                            [alignment_length] => 115
                            [identity_percentage] => 87.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.KH03IP] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.KH03IP
                            [e_value] => 4.4e-51
                            [bit_score] => 206.1
                            [alignment_length] => 107
                            [identity_percentage] => 91.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.HQ7VS1] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.HQ7VS1
                            [e_value] => 5.8e-51
                            [bit_score] => 205.7
                            [alignment_length] => 158
                            [identity_percentage] => 70.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.VX28TM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.VX28TM
                            [e_value] => 1.3e-50
                            [bit_score] => 204.5
                            [alignment_length] => 107
                            [identity_percentage] => 91.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.14G146500] => Array
                        (
                            [gene_id] => Glyma.14G146500
                            [e_value] => 4.9e-50
                            [bit_score] => 202.6
                            [alignment_length] => 313
                            [identity_percentage] => 39.6
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.6A4TC1] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.6A4TC1
                            [e_value] => 1.1e-49
                            [bit_score] => 201.4
                            [alignment_length] => 265
                            [identity_percentage] => 47.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.20G059900] => Array
                        (
                            [gene_id] => Glyma.20G059900
                            [e_value] => 3.5e-48
                            [bit_score] => 196.4
                            [alignment_length] => 295
                            [identity_percentage] => 40.0
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.07G119600] => Array
                        (
                            [gene_id] => Glyma.07G119600
                            [e_value] => 6.0e-48
                            [bit_score] => 195.7
                            [alignment_length] => 296
                            [identity_percentage] => 41.6
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.N9660C] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.N9660C
                            [e_value] => 1.3e-47
                            [bit_score] => 194.5
                            [alignment_length] => 269
                            [identity_percentage] => 46.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IPE5VY] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IPE5VY
                            [e_value] => 3.0e-47
                            [bit_score] => 193.4
                            [alignment_length] => 314
                            [identity_percentage] => 40.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.BG80MW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.BG80MW
                            [e_value] => 3.9e-47
                            [bit_score] => 193.0
                            [alignment_length] => 174
                            [identity_percentage] => 64.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.XS5DYX] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.XS5DYX
                            [e_value] => 1.9e-46
                            [bit_score] => 190.7
                            [alignment_length] => 197
                            [identity_percentage] => 52.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.14G141100] => Array
                        (
                            [gene_id] => Glyma.14G141100
                            [e_value] => 4.3e-46
                            [bit_score] => 189.5
                            [alignment_length] => 264
                            [identity_percentage] => 42.0
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IRD4WN] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IRD4WN
                            [e_value] => 1.2e-45
                            [bit_score] => 188.0
                            [alignment_length] => 142
                            [identity_percentage] => 71.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.6TZ82I] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.6TZ82I
                            [e_value] => 4.7e-45
                            [bit_score] => 186.0
                            [alignment_length] => 176
                            [identity_percentage] => 62.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Z8R2P5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Z8R2P5
                            [e_value] => 4.7e-45
                            [bit_score] => 186.0
                            [alignment_length] => 144
                            [identity_percentage] => 69.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.HZWW81] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.HZWW81
                            [e_value] => 8.0e-45
                            [bit_score] => 185.3
                            [alignment_length] => 167
                            [identity_percentage] => 56.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.MRFE53] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.MRFE53
                            [e_value] => 3.1e-44
                            [bit_score] => 183.3
                            [alignment_length] => 133
                            [identity_percentage] => 72.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.M3JTMX] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M3JTMX
                            [e_value] => 4.0e-44
                            [bit_score] => 183.0
                            [alignment_length] => 115
                            [identity_percentage] => 77.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.6D93L5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.6D93L5
                            [e_value] => 6.8e-44
                            [bit_score] => 182.2
                            [alignment_length] => 149
                            [identity_percentage] => 67.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D002858
                                )

                        )

                    [Glyma.06G232700] => Array
                        (
                            [gene_id] => Glyma.06G232700
                            [e_value] => 1.2e-43
                            [bit_score] => 181.4
                            [alignment_length] => 295
                            [identity_percentage] => 38.0
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.E2IS3L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.E2IS3L
                            [e_value] => 4.4e-43
                            [bit_score] => 179.5
                            [alignment_length] => 167
                            [identity_percentage] => 55.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj4g0013407] => Array
                        (
                            [gene_id] => Lj4g0013407
                            [e_value] => 7.5e-43
                            [bit_score] => 178.7
                            [alignment_length] => 291
                            [identity_percentage] => 37.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.9BX371] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.9BX371
                            [e_value] => 9.8e-43
                            [bit_score] => 178.3
                            [alignment_length] => 232
                            [identity_percentage] => 44.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0013168] => Array
                        (
                            [gene_id] => Lj1g0013168
                            [e_value] => 2.4e-41
                            [bit_score] => 173.7
                            [alignment_length] => 324
                            [identity_percentage] => 35.2
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.A3328F] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.A3328F
                            [e_value] => 3.2e-41
                            [bit_score] => 173.3
                            [alignment_length] => 115
                            [identity_percentage] => 71.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0018729] => Array
                        (
                            [gene_id] => Lj2g0018729
                            [e_value] => 3.2e-41
                            [bit_score] => 173.3
                            [alignment_length] => 328
                            [identity_percentage] => 37.5
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.54H83L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.54H83L
                            [e_value] => 7.1e-41
                            [bit_score] => 172.2
                            [alignment_length] => 227
                            [identity_percentage] => 46.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.T3KCYU] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.T3KCYU
                            [e_value] => 9.2e-41
                            [bit_score] => 171.8
                            [alignment_length] => 88
                            [identity_percentage] => 93.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.09G096400] => Array
                        (
                            [gene_id] => Glyma.09G096400
                            [e_value] => 9.2e-41
                            [bit_score] => 171.8
                            [alignment_length] => 307
                            [identity_percentage] => 35.8
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Y4Y8ET] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Y4Y8ET
                            [e_value] => 2.1e-40
                            [bit_score] => 170.6
                            [alignment_length] => 87
                            [identity_percentage] => 93.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D001651
                                )

                        )

                    [Lj6g0014333] => Array
                        (
                            [gene_id] => Lj6g0014333
                            [e_value] => 4.6e-40
                            [bit_score] => 169.5
                            [alignment_length] => 306
                            [identity_percentage] => 38.2
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IA7WGU] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IA7WGU
                            [e_value] => 7.8e-40
                            [bit_score] => 168.7
                            [alignment_length] => 248
                            [identity_percentage] => 46.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.APK0NP] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.APK0NP
                            [e_value] => 1.0e-39
                            [bit_score] => 168.3
                            [alignment_length] => 106
                            [identity_percentage] => 82.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.2SA9QW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.2SA9QW
                            [e_value] => 1.3e-39
                            [bit_score] => 167.9
                            [alignment_length] => 133
                            [identity_percentage] => 66.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0014614] => Array
                        (
                            [gene_id] => Lj2g0014614
                            [e_value] => 1.3e-39
                            [bit_score] => 167.9
                            [alignment_length] => 324
                            [identity_percentage] => 34.9
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0020144] => Array
                        (
                            [gene_id] => Lj1g0020144
                            [e_value] => 3.0e-39
                            [bit_score] => 166.8
                            [alignment_length] => 320
                            [identity_percentage] => 34.7
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.19G100300] => Array
                        (
                            [gene_id] => Glyma.19G100300
                            [e_value] => 6.6e-39
                            [bit_score] => 165.6
                            [alignment_length] => 297
                            [identity_percentage] => 37.4
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.14G146600] => Array
                        (
                            [gene_id] => Glyma.14G146600
                            [e_value] => 1.1e-38
                            [bit_score] => 164.9
                            [alignment_length] => 278
                            [identity_percentage] => 40.3
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.3L2L0Y] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.3L2L0Y
                            [e_value] => 1.9e-38
                            [bit_score] => 164.1
                            [alignment_length] => 234
                            [identity_percentage] => 42.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj5g0006538] => Array
                        (
                            [gene_id] => Lj5g0006538
                            [e_value] => 4.3e-38
                            [bit_score] => 162.9
                            [alignment_length] => 312
                            [identity_percentage] => 36.9
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.2EH0QW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.2EH0QW
                            [e_value] => 5.6e-38
                            [bit_score] => 162.5
                            [alignment_length] => 176
                            [identity_percentage] => 59.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.CLW9FC] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.CLW9FC
                            [e_value] => 5.6e-38
                            [bit_score] => 162.5
                            [alignment_length] => 107
                            [identity_percentage] => 76.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.QI581D] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.QI581D
                            [e_value] => 7.3e-38
                            [bit_score] => 162.2
                            [alignment_length] => 115
                            [identity_percentage] => 74.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.U4M58P] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.U4M58P
                            [e_value] => 7.3e-38
                            [bit_score] => 162.2
                            [alignment_length] => 107
                            [identity_percentage] => 77.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.0G7P3D] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.0G7P3D
                            [e_value] => 8.1e-37
                            [bit_score] => 158.7
                            [alignment_length] => 148
                            [identity_percentage] => 64.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.HB2SP5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.HB2SP5
                            [e_value] => 8.1e-37
                            [bit_score] => 158.7
                            [alignment_length] => 129
                            [identity_percentage] => 77.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.0UKE70] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.0UKE70
                            [e_value] => 1.1e-36
                            [bit_score] => 158.3
                            [alignment_length] => 167
                            [identity_percentage] => 52.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.WSML5L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.WSML5L
                            [e_value] => 1.1e-36
                            [bit_score] => 158.3
                            [alignment_length] => 177
                            [identity_percentage] => 53.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [LjContig00408g0026416] => Array
                        (
                            [gene_id] => LjContig00408g0026416
                            [e_value] => 2.3e-36
                            [bit_score] => 157.1
                            [alignment_length] => 259
                            [identity_percentage] => 37.1
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.71573I] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.71573I
                            [e_value] => 3.1e-36
                            [bit_score] => 156.8
                            [alignment_length] => 100
                            [identity_percentage] => 76.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.0G5FLV] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.0G5FLV
                            [e_value] => 2.0e-35
                            [bit_score] => 154.1
                            [alignment_length] => 105
                            [identity_percentage] => 70.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IQR40G] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IQR40G
                            [e_value] => 2.0e-35
                            [bit_score] => 154.1
                            [alignment_length] => 202
                            [identity_percentage] => 47.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.C99TYC] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.C99TYC
                            [e_value] => 2.6e-35
                            [bit_score] => 153.7
                            [alignment_length] => 115
                            [identity_percentage] => 73.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [LjContig00562g0026224] => Array
                        (
                            [gene_id] => LjContig00562g0026224
                            [e_value] => 2.2e-34
                            [bit_score] => 150.6
                            [alignment_length] => 271
                            [identity_percentage] => 39.9
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.F0AUH3] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.F0AUH3
                            [e_value] => 4.9e-34
                            [bit_score] => 149.4
                            [alignment_length] => 108
                            [identity_percentage] => 71.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.90XE5V] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.90XE5V
                            [e_value] => 6.4e-34
                            [bit_score] => 149.1
                            [alignment_length] => 126
                            [identity_percentage] => 70.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj4g0023820] => Array
                        (
                            [gene_id] => Lj4g0023820
                            [e_value] => 1.4e-33
                            [bit_score] => 147.9
                            [alignment_length] => 322
                            [identity_percentage] => 34.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.QD41U6] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.QD41U6
                            [e_value] => 4.1e-33
                            [bit_score] => 146.4
                            [alignment_length] => 116
                            [identity_percentage] => 64.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.G2V00H] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.G2V00H
                            [e_value] => 5.4e-33
                            [bit_score] => 146.0
                            [alignment_length] => 115
                            [identity_percentage] => 67.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Q6MQNA] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Q6MQNA
                            [e_value] => 7.1e-33
                            [bit_score] => 145.6
                            [alignment_length] => 92
                            [identity_percentage] => 76.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.KU6KXV] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.KU6KXV
                            [e_value] => 7.8e-32
                            [bit_score] => 142.1
                            [alignment_length] => 288
                            [identity_percentage] => 38.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.R7CRBK] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.R7CRBK
                            [e_value] => 1.7e-31
                            [bit_score] => 141.0
                            [alignment_length] => 77
                            [identity_percentage] => 88.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.11G160800] => Array
                        (
                            [gene_id] => Glyma.11G160800
                            [e_value] => 1.7e-31
                            [bit_score] => 141.0
                            [alignment_length] => 237
                            [identity_percentage] => 38.4
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.05G072900] => Array
                        (
                            [gene_id] => Glyma.05G072900
                            [e_value] => 2.3e-31
                            [bit_score] => 140.6
                            [alignment_length] => 237
                            [identity_percentage] => 38.4
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.JFJ878] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.JFJ878
                            [e_value] => 8.6e-31
                            [bit_score] => 138.7
                            [alignment_length] => 78
                            [identity_percentage] => 84.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.K0EZJ4] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.K0EZJ4
                            [e_value] => 1.1e-30
                            [bit_score] => 138.3
                            [alignment_length] => 224
                            [identity_percentage] => 42.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.659L4B] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.659L4B
                            [e_value] => 1.2e-29
                            [bit_score] => 134.8
                            [alignment_length] => 197
                            [identity_percentage] => 41.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.AV92MX] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.AV92MX
                            [e_value] => 1.4e-28
                            [bit_score] => 131.3
                            [alignment_length] => 94
                            [identity_percentage] => 67.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.VHU47D] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.VHU47D
                            [e_value] => 4.0e-28
                            [bit_score] => 129.8
                            [alignment_length] => 203
                            [identity_percentage] => 40.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G22094] => Array
                        (
                            [gene_id] => TPR.G22094
                            [e_value] => 6.8e-28
                            [bit_score] => 129.0
                            [alignment_length] => 117
                            [identity_percentage] => 51.3
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0013324] => Array
                        (
                            [gene_id] => Lj1g0013324
                            [e_value] => 8.9e-28
                            [bit_score] => 128.6
                            [alignment_length] => 303
                            [identity_percentage] => 32.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0019916] => Array
                        (
                            [gene_id] => Lj1g0019916
                            [e_value] => 8.9e-28
                            [bit_score] => 128.6
                            [alignment_length] => 303
                            [identity_percentage] => 32.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.003G148400] => Array
                        (
                            [gene_id] => Gorai.003G148400
                            [e_value] => 1.2e-27
                            [bit_score] => 128.3
                            [alignment_length] => 297
                            [identity_percentage] => 31.3
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0009331] => Array
                        (
                            [gene_id] => Lj3g0009331
                            [e_value] => 1.2e-27
                            [bit_score] => 128.3
                            [alignment_length] => 301
                            [identity_percentage] => 31.6
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0014470] => Array
                        (
                            [gene_id] => Lj3g0014470
                            [e_value] => 1.2e-27
                            [bit_score] => 128.3
                            [alignment_length] => 301
                            [identity_percentage] => 31.6
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.003G159900] => Array
                        (
                            [gene_id] => Gorai.003G159900
                            [e_value] => 2.0e-27
                            [bit_score] => 127.5
                            [alignment_length] => 276
                            [identity_percentage] => 33.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0004876] => Array
                        (
                            [gene_id] => Lj1g0004876
                            [e_value] => 2.6e-27
                            [bit_score] => 127.1
                            [alignment_length] => 270
                            [identity_percentage] => 35.9
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0017745] => Array
                        (
                            [gene_id] => Lj3g0017745
                            [e_value] => 2.6e-27
                            [bit_score] => 127.1
                            [alignment_length] => 303
                            [identity_percentage] => 31.4
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.JNB467] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.JNB467
                            [e_value] => 4.4e-27
                            [bit_score] => 126.3
                            [alignment_length] => 68
                            [identity_percentage] => 88.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.005G169400] => Array
                        (
                            [gene_id] => Gorai.005G169400
                            [e_value] => 5.8e-27
                            [bit_score] => 125.9
                            [alignment_length] => 280
                            [identity_percentage] => 32.5
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj6g0009158] => Array
                        (
                            [gene_id] => Lj6g0009158
                            [e_value] => 7.6e-27
                            [bit_score] => 125.6
                            [alignment_length] => 263
                            [identity_percentage] => 35.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [LjContig00080g0019961] => Array
                        (
                            [gene_id] => LjContig00080g0019961
                            [e_value] => 7.6e-27
                            [bit_score] => 125.6
                            [alignment_length] => 271
                            [identity_percentage] => 35.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0020463] => Array
                        (
                            [gene_id] => Lj3g0020463
                            [e_value] => 1.3e-26
                            [bit_score] => 124.8
                            [alignment_length] => 125
                            [identity_percentage] => 52.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [LjContig00506g0000245] => Array
                        (
                            [gene_id] => LjContig00506g0000245
                            [e_value] => 1.3e-26
                            [bit_score] => 124.8
                            [alignment_length] => 125
                            [identity_percentage] => 52.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj5g0012305] => Array
                        (
                            [gene_id] => Lj5g0012305
                            [e_value] => 1.7e-26
                            [bit_score] => 124.4
                            [alignment_length] => 125
                            [identity_percentage] => 51.2
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.08G289400] => Array
                        (
                            [gene_id] => Glyma.08G289400
                            [e_value] => 3.8e-26
                            [bit_score] => 123.2
                            [alignment_length] => 271
                            [identity_percentage] => 35.1
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0021112] => Array
                        (
                            [gene_id] => Lj3g0021112
                            [e_value] => 3.8e-26
                            [bit_score] => 123.2
                            [alignment_length] => 263
                            [identity_percentage] => 35.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0024906] => Array
                        (
                            [gene_id] => Lj3g0024906
                            [e_value] => 3.8e-26
                            [bit_score] => 123.2
                            [alignment_length] => 118
                            [identity_percentage] => 50.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.09G151100] => Array
                        (
                            [gene_id] => Glyma.09G151100
                            [e_value] => 6.4e-26
                            [bit_score] => 122.5
                            [alignment_length] => 227
                            [identity_percentage] => 36.1
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D001651
                                )

                        )

                    [Lj6g0015358] => Array
                        (
                            [gene_id] => Lj6g0015358
                            [e_value] => 1.1e-25
                            [bit_score] => 121.7
                            [alignment_length] => 114
                            [identity_percentage] => 50.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0025940] => Array
                        (
                            [gene_id] => Lj2g0025940
                            [e_value] => 1.9e-25
                            [bit_score] => 120.9
                            [alignment_length] => 266
                            [identity_percentage] => 31.2
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.XN6NS8] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.XN6NS8
                            [e_value] => 2.4e-25
                            [bit_score] => 120.6
                            [alignment_length] => 297
                            [identity_percentage] => 29.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0009501] => Array
                        (
                            [gene_id] => Lj2g0009501
                            [e_value] => 2.4e-25
                            [bit_score] => 120.6
                            [alignment_length] => 232
                            [identity_percentage] => 37.5
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.01G094300] => Array
                        (
                            [gene_id] => Glyma.01G094300
                            [e_value] => 3.2e-25
                            [bit_score] => 120.2
                            [alignment_length] => 85
                            [identity_percentage] => 61.2
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.1P3WRE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.1P3WRE
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                            [bit_score] => 119.8
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.W04P42] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.W04P42
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                            [bit_score] => 119.0
                            [alignment_length] => 288
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.Y1KF2B] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Y1KF2B
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                            [bit_score] => 118.6
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.BEX5HG] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.BEX5HG
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                            [bit_score] => 118.2
                            [alignment_length] => 170
                            [identity_percentage] => 51.2
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.Q72NH6] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Q72NH6
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                            [bit_score] => 118.2
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.S1Q5XH] => Array
                        (
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                            [identity_percentage] => 30.6
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.18PYUZ] => Array
                        (
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                            [bit_score] => 117.9
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.8K0ZU0] => Array
                        (
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                            [identity_percentage] => 44.1
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.I3DMP8] => Array
                        (
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                            [identity_percentage] => 30.6
                            [species] => arhy
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                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D003614
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                        )

                    [Lj1g0002293] => Array
                        (
                            [gene_id] => Lj1g0002293
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                            [bit_score] => 117.9
                            [alignment_length] => 96
                            [identity_percentage] => 58.3
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.9Y4FQ2] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.9Y4FQ2
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                            [bit_score] => 117.5
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                            [identity_percentage] => 30.6
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.I7E4L8] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.I7E4L8
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                            [bit_score] => 117.5
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IW28EF] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IW28EF
                            [e_value] => 2.7e-24
                            [bit_score] => 117.1
                            [alignment_length] => 288
                            [identity_percentage] => 30.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.GD7WFM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.GD7WFM
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                            [bit_score] => 116.7
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.N3555V] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.N3555V
                            [e_value] => 3.5e-24
                            [bit_score] => 116.7
                            [alignment_length] => 294
                            [identity_percentage] => 30.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0015392] => Array
                        (
                            [gene_id] => Lj1g0015392
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                            [bit_score] => 116.7
                            [alignment_length] => 96
                            [identity_percentage] => 57.3
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.QGF57N] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.QGF57N
                            [e_value] => 4.6e-24
                            [bit_score] => 116.3
                            [alignment_length] => 288
                            [identity_percentage] => 30.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.V0BAMU] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.V0BAMU
                            [e_value] => 4.6e-24
                            [bit_score] => 116.3
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0002189] => Array
                        (
                            [gene_id] => Lj2g0002189
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                            [bit_score] => 116.3
                            [alignment_length] => 275
                            [identity_percentage] => 31.6
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.72MBZZ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.72MBZZ
                            [e_value] => 6.0e-24
                            [bit_score] => 115.9
                            [alignment_length] => 297
                            [identity_percentage] => 29.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.756TEX] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.756TEX
                            [e_value] => 6.0e-24
                            [bit_score] => 115.9
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.HTN0Y5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.HTN0Y5
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                            [bit_score] => 115.9
                            [alignment_length] => 288
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.ZZQG32] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ZZQG32
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                            [bit_score] => 115.9
                            [alignment_length] => 288
                            [identity_percentage] => 30.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.4EM99Z] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.4EM99Z
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                            [bit_score] => 115.5
                            [alignment_length] => 288
                            [identity_percentage] => 30.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.CX12M5] => Array
                        (
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                            [e_value] => 7.8e-24
                            [bit_score] => 115.5
                            [alignment_length] => 297
                            [identity_percentage] => 28.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.N7R8CX] => Array
                        (
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                            [bit_score] => 115.5
                            [alignment_length] => 288
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.YL2BBV] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.YL2BBV
                            [e_value] => 7.8e-24
                            [bit_score] => 115.5
                            [alignment_length] => 292
                            [identity_percentage] => 30.8
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.39JP8F] => Array
                        (
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                            [bit_score] => 115.2
                            [alignment_length] => 288
                            [identity_percentage] => 30.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.5S8HU1] => Array
                        (
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                            [bit_score] => 115.2
                            [alignment_length] => 70
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                        )

                    [arahy.Tifrunner.gnm1.ann1.6U09DB] => Array
                        (
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                            [bit_score] => 114.8
                            [alignment_length] => 288
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.CIR6XW] => Array
                        (
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                            [bit_score] => 114.8
                            [alignment_length] => 288
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D003614
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                        (
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                            [bit_score] => 114.8
                            [alignment_length] => 288
                            [identity_percentage] => 30.2
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.JCQ008] => Array
                        (
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                            [bit_score] => 114.8
                            [alignment_length] => 288
                            [identity_percentage] => 30.2
                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
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                    [arahy.Tifrunner.gnm1.ann1.7I5EIZ] => Array
                        (
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                            [bit_score] => 114.4
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                            [species] => arhy
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.CVS9SJ] => Array
                        (
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                            [e_value] => 1.7e-23
                            [bit_score] => 114.4
                            [alignment_length] => 292
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                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.HEVL9E] => Array
                        (
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                            [bit_score] => 114.4
                            [alignment_length] => 288
                            [identity_percentage] => 30.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                        (
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                            [bit_score] => 114.4
                            [alignment_length] => 297
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.BYBE5B] => Array
                        (
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                            [bit_score] => 114.0
                            [alignment_length] => 297
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                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                        (
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                            [bit_score] => 114.0
                            [alignment_length] => 297
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                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
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                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.J01ZYU] => Array
                        (
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                            [bit_score] => 114.0
                            [alignment_length] => 288
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

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                    [arahy.Tifrunner.gnm1.ann1.TA1UNZ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.TA1UNZ
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                            [bit_score] => 114.0
                            [alignment_length] => 294
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                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.4JGR2S] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.4JGR2S
                            [e_value] => 3.0e-23
                            [bit_score] => 113.6
                            [alignment_length] => 137
                            [identity_percentage] => 43.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.M9M3R0] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M9M3R0
                            [e_value] => 3.0e-23
                            [bit_score] => 113.6
                            [alignment_length] => 145
                            [identity_percentage] => 45.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.RZIJ2L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.RZIJ2L
                            [e_value] => 3.0e-23
                            [bit_score] => 113.6
                            [alignment_length] => 288
                            [identity_percentage] => 29.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.013G120300] => Array
                        (
                            [gene_id] => Gorai.013G120300
                            [e_value] => 3.0e-23
                            [bit_score] => 113.6
                            [alignment_length] => 111
                            [identity_percentage] => 46.8
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.ZPS03P] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ZPS03P
                            [e_value] => 3.9e-23
                            [bit_score] => 113.2
                            [alignment_length] => 72
                            [identity_percentage] => 81.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.EUAW6M] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.EUAW6M
                            [e_value] => 5.1e-23
                            [bit_score] => 112.8
                            [alignment_length] => 87
                            [identity_percentage] => 62.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.GIY5N5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.GIY5N5
                            [e_value] => 5.1e-23
                            [bit_score] => 112.8
                            [alignment_length] => 174
                            [identity_percentage] => 45.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.UC4KU4] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.UC4KU4
                            [e_value] => 5.1e-23
                            [bit_score] => 112.8
                            [alignment_length] => 296
                            [identity_percentage] => 30.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.ZIM2T0] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ZIM2T0
                            [e_value] => 5.1e-23
                            [bit_score] => 112.8
                            [alignment_length] => 293
                            [identity_percentage] => 31.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MSTRG.8973] => Array
                        (
                            [gene_id] => MSTRG.8973
                            [e_value] => 5.1e-23
                            [bit_score] => 112.8
                            [alignment_length] => 286
                            [identity_percentage] => 31.1
                            [species] => ama
                            [common_name] => Avicennia marina
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.9F14AA] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.9F14AA
                            [e_value] => 6.6e-23
                            [bit_score] => 112.5
                            [alignment_length] => 288
                            [identity_percentage] => 30.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.EKYZ7W] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.EKYZ7W
                            [e_value] => 6.6e-23
                            [bit_score] => 112.5
                            [alignment_length] => 193
                            [identity_percentage] => 40.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.GCX1C5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.GCX1C5
                            [e_value] => 6.6e-23
                            [bit_score] => 112.5
                            [alignment_length] => 288
                            [identity_percentage] => 29.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.008G129700] => Array
                        (
                            [gene_id] => Gorai.008G129700
                            [e_value] => 6.6e-23
                            [bit_score] => 112.5
                            [alignment_length] => 100
                            [identity_percentage] => 50.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.GJ1AII] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.GJ1AII
                            [e_value] => 8.7e-23
                            [bit_score] => 112.1
                            [alignment_length] => 58
                            [identity_percentage] => 91.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0001164] => Array
                        (
                            [gene_id] => Lj3g0001164
                            [e_value] => 8.7e-23
                            [bit_score] => 112.1
                            [alignment_length] => 229
                            [identity_percentage] => 35.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.HUSQ38] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.HUSQ38
                            [e_value] => 1.1e-22
                            [bit_score] => 111.7
                            [alignment_length] => 58
                            [identity_percentage] => 91.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.QV2FY5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.QV2FY5
                            [e_value] => 1.1e-22
                            [bit_score] => 111.7
                            [alignment_length] => 58
                            [identity_percentage] => 91.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.SEYZ0I] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.SEYZ0I
                            [e_value] => 1.1e-22
                            [bit_score] => 111.7
                            [alignment_length] => 288
                            [identity_percentage] => 29.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10024098m.g] => Array
                        (
                            [gene_id] => Thhalv10024098m.g
                            [e_value] => 1.9e-22
                            [bit_score] => 110.9
                            [alignment_length] => 311
                            [identity_percentage] => 29.6
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj5g0017108] => Array
                        (
                            [gene_id] => Lj5g0017108
                            [e_value] => 1.9e-22
                            [bit_score] => 110.9
                            [alignment_length] => 229
                            [identity_percentage] => 35.4
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0019716] => Array
                        (
                            [gene_id] => Lj2g0019716
                            [e_value] => 2.5e-22
                            [bit_score] => 110.5
                            [alignment_length] => 118
                            [identity_percentage] => 46.6
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.001G201500] => Array
                        (
                            [gene_id] => Gorai.001G201500
                            [e_value] => 3.3e-22
                            [bit_score] => 110.2
                            [alignment_length] => 111
                            [identity_percentage] => 45.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.3V14JX] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.3V14JX
                            [e_value] => 4.3e-22
                            [bit_score] => 109.8
                            [alignment_length] => 58
                            [identity_percentage] => 89.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IUXR99] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IUXR99
                            [e_value] => 4.3e-22
                            [bit_score] => 109.8
                            [alignment_length] => 289
                            [identity_percentage] => 28.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.NT2WSK] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.NT2WSK
                            [e_value] => 7.3e-22
                            [bit_score] => 109.0
                            [alignment_length] => 120
                            [identity_percentage] => 49.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.005G226600] => Array
                        (
                            [gene_id] => Gorai.005G226600
                            [e_value] => 7.3e-22
                            [bit_score] => 109.0
                            [alignment_length] => 111
                            [identity_percentage] => 46.8
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.007G262100] => Array
                        (
                            [gene_id] => Gorai.007G262100
                            [e_value] => 7.3e-22
                            [bit_score] => 109.0
                            [alignment_length] => 111
                            [identity_percentage] => 45.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.013G103100] => Array
                        (
                            [gene_id] => Gorai.013G103100
                            [e_value] => 7.3e-22
                            [bit_score] => 109.0
                            [alignment_length] => 244
                            [identity_percentage] => 30.3
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.M2MFDB] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M2MFDB
                            [e_value] => 9.6e-22
                            [bit_score] => 108.6
                            [alignment_length] => 292
                            [identity_percentage] => 29.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj4g0018844] => Array
                        (
                            [gene_id] => Lj4g0018844
                            [e_value] => 9.6e-22
                            [bit_score] => 108.6
                            [alignment_length] => 86
                            [identity_percentage] => 54.7
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu015188.1] => Array
                        (
                            [gene_id] => Oeu015188.1
                            [e_value] => 9.6e-22
                            [bit_score] => 108.6
                            [alignment_length] => 301
                            [identity_percentage] => 30.6
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.NF0PPL] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.NF0PPL
                            [e_value] => 1.3e-21
                            [bit_score] => 108.2
                            [alignment_length] => 58
                            [identity_percentage] => 89.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.C39H2M] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.C39H2M
                            [e_value] => 1.6e-21
                            [bit_score] => 107.8
                            [alignment_length] => 288
                            [identity_percentage] => 29.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0012339] => Array
                        (
                            [gene_id] => Lj2g0012339
                            [e_value] => 1.6e-21
                            [bit_score] => 107.8
                            [alignment_length] => 229
                            [identity_percentage] => 34.1
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.JP535L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.JP535L
                            [e_value] => 2.1e-21
                            [bit_score] => 107.5
                            [alignment_length] => 288
                            [identity_percentage] => 29.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.DQ3ZQE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.DQ3ZQE
                            [e_value] => 2.8e-21
                            [bit_score] => 107.1
                            [alignment_length] => 288
                            [identity_percentage] => 28.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.ZMN0FL] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ZMN0FL
                            [e_value] => 4.8e-21
                            [bit_score] => 106.3
                            [alignment_length] => 288
                            [identity_percentage] => 29.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_22769_v3] => Array
                        (
                            [gene_id] => Ca_22769_v3
                            [e_value] => 4.8e-21
                            [bit_score] => 106.3
                            [alignment_length] => 96
                            [identity_percentage] => 52.1
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.68U12A] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.68U12A
                            [e_value] => 6.2e-21
                            [bit_score] => 105.9
                            [alignment_length] => 138
                            [identity_percentage] => 49.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.PYBE03] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.PYBE03
                            [e_value] => 6.2e-21
                            [bit_score] => 105.9
                            [alignment_length] => 153
                            [identity_percentage] => 40.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [CiPaw.04G053800] => Array
                        (
                            [gene_id] => CiPaw.04G053800
                            [e_value] => 6.2e-21
                            [bit_score] => 105.9
                            [alignment_length] => 291
                            [identity_percentage] => 29.6
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Z93FG5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Z93FG5
                            [e_value] => 8.1e-21
                            [bit_score] => 105.5
                            [alignment_length] => 58
                            [identity_percentage] => 86.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_07003_v3] => Array
                        (
                            [gene_id] => Ca_07003_v3
                            [e_value] => 8.1e-21
                            [bit_score] => 105.5
                            [alignment_length] => 96
                            [identity_percentage] => 52.1
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_26786_v3] => Array
                        (
                            [gene_id] => Ca_26786_v3
                            [e_value] => 8.1e-21
                            [bit_score] => 105.5
                            [alignment_length] => 96
                            [identity_percentage] => 52.1
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10012334m.g] => Array
                        (
                            [gene_id] => Thhalv10012334m.g
                            [e_value] => 8.1e-21
                            [bit_score] => 105.5
                            [alignment_length] => 256
                            [identity_percentage] => 30.1
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.W4MS58] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.W4MS58
                            [e_value] => 1.4e-20
                            [bit_score] => 104.8
                            [alignment_length] => 288
                            [identity_percentage] => 28.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu022516.1] => Array
                        (
                            [gene_id] => Oeu022516.1
                            [e_value] => 1.4e-20
                            [bit_score] => 104.8
                            [alignment_length] => 301
                            [identity_percentage] => 31.6
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.2H9LFQ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.2H9LFQ
                            [e_value] => 1.8e-20
                            [bit_score] => 104.4
                            [alignment_length] => 58
                            [identity_percentage] => 87.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.8C5ZBV] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.8C5ZBV
                            [e_value] => 1.8e-20
                            [bit_score] => 104.4
                            [alignment_length] => 58
                            [identity_percentage] => 87.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.T6DPWG] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.T6DPWG
                            [e_value] => 1.8e-20
                            [bit_score] => 104.4
                            [alignment_length] => 149
                            [identity_percentage] => 41.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G9238] => Array
                        (
                            [gene_id] => TPR.G9238
                            [e_value] => 2.4e-20
                            [bit_score] => 104.0
                            [alignment_length] => 280
                            [identity_percentage] => 27.1
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.V4TPZ0] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.V4TPZ0
                            [e_value] => 3.1e-20
                            [bit_score] => 103.6
                            [alignment_length] => 62
                            [identity_percentage] => 75.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.8UCL89] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.8UCL89
                            [e_value] => 5.3e-20
                            [bit_score] => 102.8
                            [alignment_length] => 279
                            [identity_percentage] => 28.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.848KF4] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.848KF4
                            [e_value] => 6.9e-20
                            [bit_score] => 102.4
                            [alignment_length] => 78
                            [identity_percentage] => 57.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_18984_v3] => Array
                        (
                            [gene_id] => Ca_18984_v3
                            [e_value] => 6.9e-20
                            [bit_score] => 102.4
                            [alignment_length] => 96
                            [identity_percentage] => 51.0
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Migut.O00086] => Array
                        (
                            [gene_id] => Migut.O00086
                            [e_value] => 6.9e-20
                            [bit_score] => 102.4
                            [alignment_length] => 308
                            [identity_percentage] => 25.6
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.009G307900] => Array
                        (
                            [gene_id] => Gorai.009G307900
                            [e_value] => 6.9e-20
                            [bit_score] => 102.4
                            [alignment_length] => 111
                            [identity_percentage] => 43.2
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Migut.O00085] => Array
                        (
                            [gene_id] => Migut.O00085
                            [e_value] => 9.0e-20
                            [bit_score] => 102.1
                            [alignment_length] => 308
                            [identity_percentage] => 25.6
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.9363QZ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.9363QZ
                            [e_value] => 1.2e-19
                            [bit_score] => 101.7
                            [alignment_length] => 56
                            [identity_percentage] => 87.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0000788] => Array
                        (
                            [gene_id] => Lj1g0000788
                            [e_value] => 1.2e-19
                            [bit_score] => 101.7
                            [alignment_length] => 230
                            [identity_percentage] => 34.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Q2DA23] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Q2DA23
                            [e_value] => 1.5e-19
                            [bit_score] => 101.3
                            [alignment_length] => 288
                            [identity_percentage] => 28.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MSTRG.23897] => Array
                        (
                            [gene_id] => MSTRG.23897
                            [e_value] => 2.6e-19
                            [bit_score] => 100.5
                            [alignment_length] => 77
                            [identity_percentage] => 57.1
                            [species] => ama
                            [common_name] => Avicennia marina
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.6F2NI6] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.6F2NI6
                            [e_value] => 3.4e-19
                            [bit_score] => 100.1
                            [alignment_length] => 271
                            [identity_percentage] => 30.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_04070_v3] => Array
                        (
                            [gene_id] => Ca_04070_v3
                            [e_value] => 3.4e-19
                            [bit_score] => 100.1
                            [alignment_length] => 96
                            [identity_percentage] => 51.0
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu007102.1] => Array
                        (
                            [gene_id] => Oeu007102.1
                            [e_value] => 3.4e-19
                            [bit_score] => 100.1
                            [alignment_length] => 301
                            [identity_percentage] => 29.9
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.P57W7I] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.P57W7I
                            [e_value] => 4.4e-19
                            [bit_score] => 99.8
                            [alignment_length] => 287
                            [identity_percentage] => 28.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.9IG2T4] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.9IG2T4
                            [e_value] => 5.8e-19
                            [bit_score] => 99.4
                            [alignment_length] => 58
                            [identity_percentage] => 87.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_23932_v3] => Array
                        (
                            [gene_id] => Ca_23932_v3
                            [e_value] => 5.8e-19
                            [bit_score] => 99.4
                            [alignment_length] => 96
                            [identity_percentage] => 50.0
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [C05p32790] => Array
                        (
                            [gene_id] => C05p32790
                            [e_value] => 7.6e-19
                            [bit_score] => 99.0
                            [alignment_length] => 266
                            [identity_percentage] => 29.3
                            [species] => bna
                            [common_name] => Brassica napus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.012G096500] => Array
                        (
                            [gene_id] => Gorai.012G096500
                            [e_value] => 7.6e-19
                            [bit_score] => 99.0
                            [alignment_length] => 106
                            [identity_percentage] => 45.3
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu008148.1] => Array
                        (
                            [gene_id] => Oeu008148.1
                            [e_value] => 7.6e-19
                            [bit_score] => 99.0
                            [alignment_length] => 301
                            [identity_percentage] => 29.2
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [Oeu064343.1] => Array
                        (
                            [gene_id] => Oeu064343.1
                            [e_value] => 7.6e-19
                            [bit_score] => 99.0
                            [alignment_length] => 291
                            [identity_percentage] => 30.9
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [Ca_03828_v3] => Array
                        (
                            [gene_id] => Ca_03828_v3
                            [e_value] => 1.3e-18
                            [bit_score] => 98.2
                            [alignment_length] => 96
                            [identity_percentage] => 49.0
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_19597_v3] => Array
                        (
                            [gene_id] => Ca_19597_v3
                            [e_value] => 1.3e-18
                            [bit_score] => 98.2
                            [alignment_length] => 99
                            [identity_percentage] => 46.5
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.007G206600] => Array
                        (
                            [gene_id] => Gorai.007G206600
                            [e_value] => 1.7e-18
                            [bit_score] => 97.8
                            [alignment_length] => 100
                            [identity_percentage] => 43.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.07G173200] => Array
                        (
                            [gene_id] => Glyma.07G173200
                            [e_value] => 2.2e-18
                            [bit_score] => 97.4
                            [alignment_length] => 60
                            [identity_percentage] => 71.7
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D001651
                                )

                        )

                    [Glyma.18G122300] => Array
                        (
                            [gene_id] => Glyma.18G122300
                            [e_value] => 2.9e-18
                            [bit_score] => 97.1
                            [alignment_length] => 174
                            [identity_percentage] => 35.1
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [HanXRQChr02g0042331] => Array
                        (
                            [gene_id] => HanXRQChr02g0042331
                            [e_value] => 6.4e-18
                            [bit_score] => 95.9
                            [alignment_length] => 304
                            [identity_percentage] => 29.6
                            [species] => han
                            [common_name] => Helianthus annuus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.LSKZ83] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.LSKZ83
                            [e_value] => 8.4e-18
                            [bit_score] => 95.5
                            [alignment_length] => 58
                            [identity_percentage] => 74.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ca_03988_v3] => Array
                        (
                            [gene_id] => Ca_03988_v3
                            [e_value] => 8.4e-18
                            [bit_score] => 95.5
                            [alignment_length] => 96
                            [identity_percentage] => 47.9
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.003G115300] => Array
                        (
                            [gene_id] => Gorai.003G115300
                            [e_value] => 8.4e-18
                            [bit_score] => 95.5
                            [alignment_length] => 80
                            [identity_percentage] => 52.5
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.N3AN7R] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.N3AN7R
                            [e_value] => 1.1e-17
                            [bit_score] => 95.1
                            [alignment_length] => 55
                            [identity_percentage] => 80.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [HanXRQChr11g0333631] => Array
                        (
                            [gene_id] => HanXRQChr11g0333631
                            [e_value] => 1.1e-17
                            [bit_score] => 95.1
                            [alignment_length] => 299
                            [identity_percentage] => 29.4
                            [species] => han
                            [common_name] => Helianthus annuus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Migut.O00084] => Array
                        (
                            [gene_id] => Migut.O00084
                            [e_value] => 1.4e-17
                            [bit_score] => 94.7
                            [alignment_length] => 292
                            [identity_percentage] => 25.7
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.PGH66G] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.PGH66G
                            [e_value] => 2.4e-17
                            [bit_score] => 94.0
                            [alignment_length] => 50
                            [identity_percentage] => 88.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.06G202700] => Array
                        (
                            [gene_id] => Glyma.06G202700
                            [e_value] => 2.4e-17
                            [bit_score] => 94.0
                            [alignment_length] => 99
                            [identity_percentage] => 45.5
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.S13B92] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.S13B92
                            [e_value] => 3.2e-17
                            [bit_score] => 93.6
                            [alignment_length] => 49
                            [identity_percentage] => 91.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.WB5STR] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.WB5STR
                            [e_value] => 4.2e-17
                            [bit_score] => 93.2
                            [alignment_length] => 95
                            [identity_percentage] => 51.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.UNLN87] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.UNLN87
                            [e_value] => 7.1e-17
                            [bit_score] => 92.4
                            [alignment_length] => 58
                            [identity_percentage] => 72.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10024111m.g] => Array
                        (
                            [gene_id] => Thhalv10024111m.g
                            [e_value] => 7.1e-17
                            [bit_score] => 92.4
                            [alignment_length] => 77
                            [identity_percentage] => 49.4
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Solyc07g025280.1] => Array
                        (
                            [gene_id] => Solyc07g025280.1
                            [e_value] => 7.1e-17
                            [bit_score] => 92.4
                            [alignment_length] => 103
                            [identity_percentage] => 41.7
                            [species] => sly
                            [common_name] => Solanum lycopersicum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Migut.O00081] => Array
                        (
                            [gene_id] => Migut.O00081
                            [e_value] => 9.3e-17
                            [bit_score] => 92.0
                            [alignment_length] => 287
                            [identity_percentage] => 25.8
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.013G130000] => Array
                        (
                            [gene_id] => Gorai.013G130000
                            [e_value] => 1.6e-16
                            [bit_score] => 91.3
                            [alignment_length] => 234
                            [identity_percentage] => 28.6
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D001651
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Q4LR9P] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Q4LR9P
                            [e_value] => 2.1e-16
                            [bit_score] => 90.9
                            [alignment_length] => 58
                            [identity_percentage] => 72.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10002268m.g] => Array
                        (
                            [gene_id] => Thhalv10002268m.g
                            [e_value] => 2.1e-16
                            [bit_score] => 90.9
                            [alignment_length] => 124
                            [identity_percentage] => 37.9
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.0VPI4Y] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.0VPI4Y
                            [e_value] => 2.7e-16
                            [bit_score] => 90.5
                            [alignment_length] => 288
                            [identity_percentage] => 27.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C026718.2] => Array
                        (
                            [gene_id] => MELO3C026718.2
                            [e_value] => 2.7e-16
                            [bit_score] => 90.5
                            [alignment_length] => 298
                            [identity_percentage] => 25.2
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Thhalv10002329m.g] => Array
                        (
                            [gene_id] => Thhalv10002329m.g
                            [e_value] => 2.7e-16
                            [bit_score] => 90.5
                            [alignment_length] => 198
                            [identity_percentage] => 30.3
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.001G087300] => Array
                        (
                            [gene_id] => Gorai.001G087300
                            [e_value] => 2.7e-16
                            [bit_score] => 90.5
                            [alignment_length] => 80
                            [identity_percentage] => 48.8
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.0IRR4S] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.0IRR4S
                            [e_value] => 3.5e-16
                            [bit_score] => 90.1
                            [alignment_length] => 269
                            [identity_percentage] => 28.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [CAN.G362.35] => Array
                        (
                            [gene_id] => CAN.G362.35
                            [e_value] => 3.5e-16
                            [bit_score] => 90.1
                            [alignment_length] => 79
                            [identity_percentage] => 49.4
                            [species] => can
                            [common_name] => Capsicum annuum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.I58UVB] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.I58UVB
                            [e_value] => 6.0e-16
                            [bit_score] => 89.4
                            [alignment_length] => 277
                            [identity_percentage] => 28.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.14KCD6] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.14KCD6
                            [e_value] => 7.9e-16
                            [bit_score] => 89.0
                            [alignment_length] => 223
                            [identity_percentage] => 30.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.KK5I4J] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.KK5I4J
                            [e_value] => 1.0e-15
                            [bit_score] => 88.6
                            [alignment_length] => 42
                            [identity_percentage] => 95.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.45JVR9] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.45JVR9
                            [e_value] => 1.3e-15
                            [bit_score] => 88.2
                            [alignment_length] => 58
                            [identity_percentage] => 69.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C004850.2] => Array
                        (
                            [gene_id] => MELO3C004850.2
                            [e_value] => 1.7e-15
                            [bit_score] => 87.8
                            [alignment_length] => 298
                            [identity_percentage] => 23.8
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Hund20235] => Array
                        (
                            [gene_id] => Hund20235
                            [e_value] => 2.3e-15
                            [bit_score] => 87.4
                            [alignment_length] => 339
                            [identity_percentage] => 26.3
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.17G002683] => Array
                        (
                            [gene_id] => Manes.17G002683
                            [e_value] => 3.0e-15
                            [bit_score] => 87.0
                            [alignment_length] => 97
                            [identity_percentage] => 41.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.20G030000] => Array
                        (
                            [gene_id] => Glyma.20G030000
                            [e_value] => 3.9e-15
                            [bit_score] => 86.7
                            [alignment_length] => 58
                            [identity_percentage] => 62.1
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D001651
                                )

                        )

                    [Thhalv10001275m.g] => Array
                        (
                            [gene_id] => Thhalv10001275m.g
                            [e_value] => 5.1e-15
                            [bit_score] => 86.3
                            [alignment_length] => 113
                            [identity_percentage] => 36.3
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.18G156400] => Array
                        (
                            [gene_id] => Glyma.18G156400
                            [e_value] => 5.1e-15
                            [bit_score] => 86.3
                            [alignment_length] => 79
                            [identity_percentage] => 51.9
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.17G018812] => Array
                        (
                            [gene_id] => Manes.17G018812
                            [e_value] => 5.1e-15
                            [bit_score] => 86.3
                            [alignment_length] => 97
                            [identity_percentage] => 40.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.06G001751] => Array
                        (
                            [gene_id] => Manes.06G001751
                            [e_value] => 6.6e-15
                            [bit_score] => 85.9
                            [alignment_length] => 109
                            [identity_percentage] => 38.5
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [ClCG03G013730] => Array
                        (
                            [gene_id] => ClCG03G013730
                            [e_value] => 8.7e-15
                            [bit_score] => 85.5
                            [alignment_length] => 296
                            [identity_percentage] => 24.0
                            [species] => cla
                            [common_name] => Citrullus lanatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000002
                                )

                        )

                    [Manes.05G131901] => Array
                        (
                            [gene_id] => Manes.05G131901
                            [e_value] => 8.7e-15
                            [bit_score] => 85.5
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.16G055925] => Array
                        (
                            [gene_id] => Manes.16G055925
                            [e_value] => 1.1e-14
                            [bit_score] => 85.1
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10009827m.g] => Array
                        (
                            [gene_id] => Thhalv10009827m.g
                            [e_value] => 1.5e-14
                            [bit_score] => 84.7
                            [alignment_length] => 98
                            [identity_percentage] => 39.8
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [LjContig00155g0016901] => Array
                        (
                            [gene_id] => LjContig00155g0016901
                            [e_value] => 1.5e-14
                            [bit_score] => 84.7
                            [alignment_length] => 92
                            [identity_percentage] => 44.6
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [CiPaw.08G029600] => Array
                        (
                            [gene_id] => CiPaw.08G029600
                            [e_value] => 1.9e-14
                            [bit_score] => 84.3
                            [alignment_length] => 304
                            [identity_percentage] => 28.9
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen12g001100] => Array
                        (
                            [gene_id] => Sopen12g001100
                            [e_value] => 1.9e-14
                            [bit_score] => 84.3
                            [alignment_length] => 285
                            [identity_percentage] => 26.0
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.7A5GZE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.7A5GZE
                            [e_value] => 2.5e-14
                            [bit_score] => 84.0
                            [alignment_length] => 98
                            [identity_percentage] => 44.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.09G089621] => Array
                        (
                            [gene_id] => Manes.09G089621
                            [e_value] => 2.5e-14
                            [bit_score] => 84.0
                            [alignment_length] => 288
                            [identity_percentage] => 26.0
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000002
                                )

                        )

                    [Manes.16G057426] => Array
                        (
                            [gene_id] => Manes.16G057426
                            [e_value] => 2.5e-14
                            [bit_score] => 84.0
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.1RY5L5] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.1RY5L5
                            [e_value] => 3.3e-14
                            [bit_score] => 83.6
                            [alignment_length] => 98
                            [identity_percentage] => 44.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.13G076999] => Array
                        (
                            [gene_id] => Manes.13G076999
                            [e_value] => 3.3e-14
                            [bit_score] => 83.6
                            [alignment_length] => 97
                            [identity_percentage] => 43.3
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.S095214] => Array
                        (
                            [gene_id] => Manes.S095214
                            [e_value] => 3.3e-14
                            [bit_score] => 83.6
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.558G8J] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.558G8J
                            [e_value] => 4.3e-14
                            [bit_score] => 83.2
                            [alignment_length] => 98
                            [identity_percentage] => 44.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.A5BTLM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.A5BTLM
                            [e_value] => 4.3e-14
                            [bit_score] => 83.2
                            [alignment_length] => 98
                            [identity_percentage] => 44.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IM0SRD] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IM0SRD
                            [e_value] => 4.3e-14
                            [bit_score] => 83.2
                            [alignment_length] => 104
                            [identity_percentage] => 43.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.GI390R] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.GI390R
                            [e_value] => 5.6e-14
                            [bit_score] => 82.8
                            [alignment_length] => 52
                            [identity_percentage] => 73.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu064527.1] => Array
                        (
                            [gene_id] => Oeu064527.1
                            [e_value] => 5.6e-14
                            [bit_score] => 82.8
                            [alignment_length] => 284
                            [identity_percentage] => 29.9
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.H8F1EK] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.H8F1EK
                            [e_value] => 7.3e-14
                            [bit_score] => 82.4
                            [alignment_length] => 59
                            [identity_percentage] => 67.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.010G157800] => Array
                        (
                            [gene_id] => Gorai.010G157800
                            [e_value] => 7.3e-14
                            [bit_score] => 82.4
                            [alignment_length] => 88
                            [identity_percentage] => 44.3
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.96HYEI] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.96HYEI
                            [e_value] => 9.6e-14
                            [bit_score] => 82.0
                            [alignment_length] => 98
                            [identity_percentage] => 42.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.KY4VPW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.KY4VPW
                            [e_value] => 9.6e-14
                            [bit_score] => 82.0
                            [alignment_length] => 98
                            [identity_percentage] => 44.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.WI178G] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.WI178G
                            [e_value] => 9.6e-14
                            [bit_score] => 82.0
                            [alignment_length] => 95
                            [identity_percentage] => 44.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.10G080301] => Array
                        (
                            [gene_id] => Manes.10G080301
                            [e_value] => 9.6e-14
                            [bit_score] => 82.0
                            [alignment_length] => 97
                            [identity_percentage] => 41.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.MH5L6C] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.MH5L6C
                            [e_value] => 1.3e-13
                            [bit_score] => 81.6
                            [alignment_length] => 98
                            [identity_percentage] => 43.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.07G055364] => Array
                        (
                            [gene_id] => Manes.07G055364
                            [e_value] => 1.3e-13
                            [bit_score] => 81.6
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.07G055686] => Array
                        (
                            [gene_id] => Manes.07G055686
                            [e_value] => 1.3e-13
                            [bit_score] => 81.6
                            [alignment_length] => 97
                            [identity_percentage] => 43.3
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.11G096250] => Array
                        (
                            [gene_id] => Manes.11G096250
                            [e_value] => 1.3e-13
                            [bit_score] => 81.6
                            [alignment_length] => 97
                            [identity_percentage] => 41.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.C9QDYM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.C9QDYM
                            [e_value] => 1.6e-13
                            [bit_score] => 81.3
                            [alignment_length] => 83
                            [identity_percentage] => 50.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.GQ521E] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.GQ521E
                            [e_value] => 1.6e-13
                            [bit_score] => 81.3
                            [alignment_length] => 287
                            [identity_percentage] => 26.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.PC7CW8] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.PC7CW8
                            [e_value] => 1.6e-13
                            [bit_score] => 81.3
                            [alignment_length] => 98
                            [identity_percentage] => 43.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.008G169100] => Array
                        (
                            [gene_id] => Gorai.008G169100
                            [e_value] => 1.6e-13
                            [bit_score] => 81.3
                            [alignment_length] => 269
                            [identity_percentage] => 27.1
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.8102HM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.8102HM
                            [e_value] => 2.1e-13
                            [bit_score] => 80.9
                            [alignment_length] => 98
                            [identity_percentage] => 43.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.BYA8HJ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.BYA8HJ
                            [e_value] => 2.1e-13
                            [bit_score] => 80.9
                            [alignment_length] => 98
                            [identity_percentage] => 42.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.10G055732] => Array
                        (
                            [gene_id] => Manes.10G055732
                            [e_value] => 2.1e-13
                            [bit_score] => 80.9
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.97NBY2] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.97NBY2
                            [e_value] => 2.8e-13
                            [bit_score] => 80.5
                            [alignment_length] => 98
                            [identity_percentage] => 42.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.M3KMZQ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M3KMZQ
                            [e_value] => 2.8e-13
                            [bit_score] => 80.5
                            [alignment_length] => 98
                            [identity_percentage] => 43.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.V7R3VA] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.V7R3VA
                            [e_value] => 2.8e-13
                            [bit_score] => 80.5
                            [alignment_length] => 44
                            [identity_percentage] => 84.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [CiPaw.03G092700] => Array
                        (
                            [gene_id] => CiPaw.03G092700
                            [e_value] => 2.8e-13
                            [bit_score] => 80.5
                            [alignment_length] => 319
                            [identity_percentage] => 26.3
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D002858
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.CI6B6W] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.CI6B6W
                            [e_value] => 3.6e-13
                            [bit_score] => 80.1
                            [alignment_length] => 52
                            [identity_percentage] => 71.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [ClCG10G003450] => Array
                        (
                            [gene_id] => ClCG10G003450
                            [e_value] => 3.6e-13
                            [bit_score] => 80.1
                            [alignment_length] => 298
                            [identity_percentage] => 23.2
                            [species] => cla
                            [common_name] => Citrullus lanatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000002
                                )

                        )

                    [Lj5g0027822] => Array
                        (
                            [gene_id] => Lj5g0027822
                            [e_value] => 3.6e-13
                            [bit_score] => 80.1
                            [alignment_length] => 92
                            [identity_percentage] => 44.6
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.07G056008] => Array
                        (
                            [gene_id] => Manes.07G056008
                            [e_value] => 3.6e-13
                            [bit_score] => 80.1
                            [alignment_length] => 97
                            [identity_percentage] => 42.3
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.THNS6P] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.THNS6P
                            [e_value] => 4.8e-13
                            [bit_score] => 79.7
                            [alignment_length] => 59
                            [identity_percentage] => 64.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [CiPaw.01G104600] => Array
                        (
                            [gene_id] => CiPaw.01G104600
                            [e_value] => 4.8e-13
                            [bit_score] => 79.7
                            [alignment_length] => 107
                            [identity_percentage] => 41.1
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.001G115800] => Array
                        (
                            [gene_id] => Gorai.001G115800
                            [e_value] => 4.8e-13
                            [bit_score] => 79.7
                            [alignment_length] => 312
                            [identity_percentage] => 23.7
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Migut.H01165] => Array
                        (
                            [gene_id] => Migut.H01165
                            [e_value] => 6.2e-13
                            [bit_score] => 79.3
                            [alignment_length] => 122
                            [identity_percentage] => 33.6
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10023048m.g] => Array
                        (
                            [gene_id] => Thhalv10023048m.g
                            [e_value] => 6.2e-13
                            [bit_score] => 79.3
                            [alignment_length] => 77
                            [identity_percentage] => 42.9
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.1Y1G78] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.1Y1G78
                            [e_value] => 8.1e-13
                            [bit_score] => 79.0
                            [alignment_length] => 98
                            [identity_percentage] => 42.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.IJ0KFI] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.IJ0KFI
                            [e_value] => 8.1e-13
                            [bit_score] => 79.0
                            [alignment_length] => 50
                            [identity_percentage] => 70.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10023798m.g] => Array
                        (
                            [gene_id] => Thhalv10023798m.g
                            [e_value] => 1.1e-12
                            [bit_score] => 78.6
                            [alignment_length] => 320
                            [identity_percentage] => 27.5
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0026464] => Array
                        (
                            [gene_id] => Lj1g0026464
                            [e_value] => 1.1e-12
                            [bit_score] => 78.6
                            [alignment_length] => 93
                            [identity_percentage] => 46.2
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Hund08072] => Array
                        (
                            [gene_id] => Hund08072
                            [e_value] => 1.1e-12
                            [bit_score] => 78.6
                            [alignment_length] => 122
                            [identity_percentage] => 33.6
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.ASBC4P] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ASBC4P
                            [e_value] => 1.4e-12
                            [bit_score] => 78.2
                            [alignment_length] => 98
                            [identity_percentage] => 40.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.QZ4HHM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.QZ4HHM
                            [e_value] => 1.4e-12
                            [bit_score] => 78.2
                            [alignment_length] => 86
                            [identity_percentage] => 45.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G39902] => Array
                        (
                            [gene_id] => TPR.G39902
                            [e_value] => 1.4e-12
                            [bit_score] => 78.2
                            [alignment_length] => 94
                            [identity_percentage] => 40.4
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Y9U40M] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Y9U40M
                            [e_value] => 1.8e-12
                            [bit_score] => 77.8
                            [alignment_length] => 255
                            [identity_percentage] => 27.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Y76A0X] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Y76A0X
                            [e_value] => 3.1e-12
                            [bit_score] => 77.0
                            [alignment_length] => 138
                            [identity_percentage] => 40.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Hma1.2p1_0106F.1_g050930] => Array
                        (
                            [gene_id] => Hma1.2p1_0106F.1_g050930
                            [e_value] => 3.1e-12
                            [bit_score] => 77.0
                            [alignment_length] => 87
                            [identity_percentage] => 41.4
                            [species] => hma
                            [common_name] => Hydrangea macrophylla
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu048057.1] => Array
                        (
                            [gene_id] => Oeu048057.1
                            [e_value] => 3.1e-12
                            [bit_score] => 77.0
                            [alignment_length] => 264
                            [identity_percentage] => 28.4
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Ah.04g160570] => Array
                        (
                            [gene_id] => Ah.04g160570
                            [e_value] => 5.3e-12
                            [bit_score] => 76.3
                            [alignment_length] => 109
                            [identity_percentage] => 37.6
                            [species] => amhyb
                            [common_name] => Amaranthus hybridus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.QJ2VLW] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.QJ2VLW
                            [e_value] => 5.3e-12
                            [bit_score] => 76.3
                            [alignment_length] => 115
                            [identity_percentage] => 40.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G16515] => Array
                        (
                            [gene_id] => TPR.G16515
                            [e_value] => 5.3e-12
                            [bit_score] => 76.3
                            [alignment_length] => 96
                            [identity_percentage] => 38.5
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.002G201500] => Array
                        (
                            [gene_id] => Gorai.002G201500
                            [e_value] => 6.9e-12
                            [bit_score] => 75.9
                            [alignment_length] => 104
                            [identity_percentage] => 37.5
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.003G084600] => Array
                        (
                            [gene_id] => Gorai.003G084600
                            [e_value] => 6.9e-12
                            [bit_score] => 75.9
                            [alignment_length] => 66
                            [identity_percentage] => 53.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Hma1.2p1_0213F.1_g090600] => Array
                        (
                            [gene_id] => Hma1.2p1_0213F.1_g090600
                            [e_value] => 9.0e-12
                            [bit_score] => 75.5
                            [alignment_length] => 87
                            [identity_percentage] => 41.4
                            [species] => hma
                            [common_name] => Hydrangea macrophylla
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G30711] => Array
                        (
                            [gene_id] => TPR.G30711
                            [e_value] => 9.0e-12
                            [bit_score] => 75.5
                            [alignment_length] => 65
                            [identity_percentage] => 56.9
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G39624] => Array
                        (
                            [gene_id] => TPR.G39624
                            [e_value] => 9.0e-12
                            [bit_score] => 75.5
                            [alignment_length] => 96
                            [identity_percentage] => 38.5
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.7FSK73] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.7FSK73
                            [e_value] => 1.2e-11
                            [bit_score] => 75.1
                            [alignment_length] => 98
                            [identity_percentage] => 41.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.QJW6VR] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.QJW6VR
                            [e_value] => 1.2e-11
                            [bit_score] => 75.1
                            [alignment_length] => 98
                            [identity_percentage] => 41.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen01g014030] => Array
                        (
                            [gene_id] => Sopen01g014030
                            [e_value] => 1.2e-11
                            [bit_score] => 75.1
                            [alignment_length] => 300
                            [identity_percentage] => 25.3
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G10845] => Array
                        (
                            [gene_id] => TPR.G10845
                            [e_value] => 1.2e-11
                            [bit_score] => 75.1
                            [alignment_length] => 96
                            [identity_percentage] => 38.5
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G40709] => Array
                        (
                            [gene_id] => TPR.G40709
                            [e_value] => 1.5e-11
                            [bit_score] => 74.7
                            [alignment_length] => 96
                            [identity_percentage] => 38.5
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.65T66L] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.65T66L
                            [e_value] => 2.0e-11
                            [bit_score] => 74.3
                            [alignment_length] => 39
                            [identity_percentage] => 92.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Q40EC9] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Q40EC9
                            [e_value] => 2.6e-11
                            [bit_score] => 73.9
                            [alignment_length] => 98
                            [identity_percentage] => 42.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.T0AVIE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.T0AVIE
                            [e_value] => 2.6e-11
                            [bit_score] => 73.9
                            [alignment_length] => 262
                            [identity_percentage] => 26.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.010G130200] => Array
                        (
                            [gene_id] => Gorai.010G130200
                            [e_value] => 2.6e-11
                            [bit_score] => 73.9
                            [alignment_length] => 207
                            [identity_percentage] => 26.1
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [LjContig00272g0003804] => Array
                        (
                            [gene_id] => LjContig00272g0003804
                            [e_value] => 2.6e-11
                            [bit_score] => 73.9
                            [alignment_length] => 101
                            [identity_percentage] => 42.6
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C013380.2] => Array
                        (
                            [gene_id] => MELO3C013380.2
                            [e_value] => 4.5e-11
                            [bit_score] => 73.2
                            [alignment_length] => 97
                            [identity_percentage] => 34.0
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Hund12297] => Array
                        (
                            [gene_id] => Hund12297
                            [e_value] => 4.5e-11
                            [bit_score] => 73.2
                            [alignment_length] => 112
                            [identity_percentage] => 36.6
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D002662
                                )

                        )

                    [Sopen02g001730] => Array
                        (
                            [gene_id] => Sopen02g001730
                            [e_value] => 5.8e-11
                            [bit_score] => 72.8
                            [alignment_length] => 293
                            [identity_percentage] => 25.3
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.53R2A7] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.53R2A7
                            [e_value] => 7.6e-11
                            [bit_score] => 72.4
                            [alignment_length] => 74
                            [identity_percentage] => 45.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.I9EK5P] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.I9EK5P
                            [e_value] => 7.6e-11
                            [bit_score] => 72.4
                            [alignment_length] => 78
                            [identity_percentage] => 43.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.004G224200] => Array
                        (
                            [gene_id] => Gorai.004G224200
                            [e_value] => 7.6e-11
                            [bit_score] => 72.4
                            [alignment_length] => 79
                            [identity_percentage] => 43.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu045360.1] => Array
                        (
                            [gene_id] => Oeu045360.1
                            [e_value] => 7.6e-11
                            [bit_score] => 72.4
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [Sopen10g010850] => Array
                        (
                            [gene_id] => Sopen10g010850
                            [e_value] => 7.6e-11
                            [bit_score] => 72.4
                            [alignment_length] => 98
                            [identity_percentage] => 36.7
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.DFQR10] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.DFQR10
                            [e_value] => 9.9e-11
                            [bit_score] => 72.0
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.006G001200] => Array
                        (
                            [gene_id] => Gorai.006G001200
                            [e_value] => 9.9e-11
                            [bit_score] => 72.0
                            [alignment_length] => 66
                            [identity_percentage] => 50.0
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0003660g0020] => Array
                        (
                            [gene_id] => Nitab4.5_0003660g0020
                            [e_value] => 9.9e-11
                            [bit_score] => 72.0
                            [alignment_length] => 75
                            [identity_percentage] => 46.7
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D009165
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.82YQT6] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.82YQT6
                            [e_value] => 1.3e-10
                            [bit_score] => 71.6
                            [alignment_length] => 74
                            [identity_percentage] => 45.9
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C028612.2] => Array
                        (
                            [gene_id] => MELO3C028612.2
                            [e_value] => 1.3e-10
                            [bit_score] => 71.6
                            [alignment_length] => 97
                            [identity_percentage] => 34.0
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Nitab4.5_0003927g0030] => Array
                        (
                            [gene_id] => Nitab4.5_0003927g0030
                            [e_value] => 1.3e-10
                            [bit_score] => 71.6
                            [alignment_length] => 117
                            [identity_percentage] => 36.8
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000139
                                    [ORTHOFAM] => ORTHO05D000103
                                )

                        )

                    [Sopen11g016230] => Array
                        (
                            [gene_id] => Sopen11g016230
                            [e_value] => 1.3e-10
                            [bit_score] => 71.6
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G35396] => Array
                        (
                            [gene_id] => TPR.G35396
                            [e_value] => 1.3e-10
                            [bit_score] => 71.6
                            [alignment_length] => 91
                            [identity_percentage] => 38.5
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.4E97LE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.4E97LE
                            [e_value] => 1.7e-10
                            [bit_score] => 71.2
                            [alignment_length] => 74
                            [identity_percentage] => 44.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C008564.2] => Array
                        (
                            [gene_id] => MELO3C008564.2
                            [e_value] => 1.7e-10
                            [bit_score] => 71.2
                            [alignment_length] => 97
                            [identity_percentage] => 34.0
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Gorai.001G169900] => Array
                        (
                            [gene_id] => Gorai.001G169900
                            [e_value] => 1.7e-10
                            [bit_score] => 71.2
                            [alignment_length] => 66
                            [identity_percentage] => 48.5
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.1S4DUK] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.1S4DUK
                            [e_value] => 2.2e-10
                            [bit_score] => 70.9
                            [alignment_length] => 40
                            [identity_percentage] => 80.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.MZPE9F] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.MZPE9F
                            [e_value] => 2.2e-10
                            [bit_score] => 70.9
                            [alignment_length] => 65
                            [identity_percentage] => 47.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.S1M30Y] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.S1M30Y
                            [e_value] => 2.2e-10
                            [bit_score] => 70.9
                            [alignment_length] => 94
                            [identity_percentage] => 40.4
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C022767.2] => Array
                        (
                            [gene_id] => MELO3C022767.2
                            [e_value] => 2.2e-10
                            [bit_score] => 70.9
                            [alignment_length] => 97
                            [identity_percentage] => 33.0
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [MELO3C032329.2] => Array
                        (
                            [gene_id] => MELO3C032329.2
                            [e_value] => 3.8e-10
                            [bit_score] => 70.1
                            [alignment_length] => 97
                            [identity_percentage] => 34.0
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Hund10648] => Array
                        (
                            [gene_id] => Hund10648
                            [e_value] => 3.8e-10
                            [bit_score] => 70.1
                            [alignment_length] => 95
                            [identity_percentage] => 35.8
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen09g014910] => Array
                        (
                            [gene_id] => Sopen09g014910
                            [e_value] => 3.8e-10
                            [bit_score] => 70.1
                            [alignment_length] => 97
                            [identity_percentage] => 39.2
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [TPR.G3937] => Array
                        (
                            [gene_id] => TPR.G3937
                            [e_value] => 3.8e-10
                            [bit_score] => 70.1
                            [alignment_length] => 100
                            [identity_percentage] => 37.0
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.P29BXD] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.P29BXD
                            [e_value] => 6.4e-10
                            [bit_score] => 69.3
                            [alignment_length] => 118
                            [identity_percentage] => 39.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MBI17_g11095_MAGBIO] => Array
                        (
                            [gene_id] => MBI17_g11095_MAGBIO
                            [e_value] => 6.4e-10
                            [bit_score] => 69.3
                            [alignment_length] => 121
                            [identity_percentage] => 33.1
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [CiPaw.03G066400] => Array
                        (
                            [gene_id] => CiPaw.03G066400
                            [e_value] => 8.4e-10
                            [bit_score] => 68.9
                            [alignment_length] => 72
                            [identity_percentage] => 43.1
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.ZV0DC7] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.ZV0DC7
                            [e_value] => 1.1e-09
                            [bit_score] => 68.6
                            [alignment_length] => 97
                            [identity_percentage] => 40.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Manes.04G156550] => Array
                        (
                            [gene_id] => Manes.04G156550
                            [e_value] => 1.1e-09
                            [bit_score] => 68.6
                            [alignment_length] => 75
                            [identity_percentage] => 38.7
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen04g017720] => Array
                        (
                            [gene_id] => Sopen04g017720
                            [e_value] => 1.1e-09
                            [bit_score] => 68.6
                            [alignment_length] => 91
                            [identity_percentage] => 38.5
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen07g010610] => Array
                        (
                            [gene_id] => Sopen07g010610
                            [e_value] => 1.1e-09
                            [bit_score] => 68.6
                            [alignment_length] => 97
                            [identity_percentage] => 38.1
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen09g015640] => Array
                        (
                            [gene_id] => Sopen09g015640
                            [e_value] => 1.4e-09
                            [bit_score] => 68.2
                            [alignment_length] => 290
                            [identity_percentage] => 24.8
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.MQQ5HT] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.MQQ5HT
                            [e_value] => 1.9e-09
                            [bit_score] => 67.8
                            [alignment_length] => 243
                            [identity_percentage] => 25.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.011G163800] => Array
                        (
                            [gene_id] => Gorai.011G163800
                            [e_value] => 1.9e-09
                            [bit_score] => 67.8
                            [alignment_length] => 92
                            [identity_percentage] => 39.1
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Hund10602] => Array
                        (
                            [gene_id] => Hund10602
                            [e_value] => 1.9e-09
                            [bit_score] => 67.8
                            [alignment_length] => 122
                            [identity_percentage] => 28.7
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Y1GSKA] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Y1GSKA
                            [e_value] => 2.4e-09
                            [bit_score] => 67.4
                            [alignment_length] => 61
                            [identity_percentage] => 62.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C003851.2] => Array
                        (
                            [gene_id] => MELO3C003851.2
                            [e_value] => 2.4e-09
                            [bit_score] => 67.4
                            [alignment_length] => 266
                            [identity_percentage] => 25.2
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Gorai.005G125200] => Array
                        (
                            [gene_id] => Gorai.005G125200
                            [e_value] => 2.4e-09
                            [bit_score] => 67.4
                            [alignment_length] => 55
                            [identity_percentage] => 56.4
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [QL07p026138] => Array
                        (
                            [gene_id] => QL07p026138
                            [e_value] => 2.4e-09
                            [bit_score] => 67.4
                            [alignment_length] => 250
                            [identity_percentage] => 28.0
                            [species] => qlo
                            [common_name] => Quercus lobata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D004834
                                    [ORTHOFAM] => ORTHO05D006247
                                )

                        )

                    [TPR.G40697] => Array
                        (
                            [gene_id] => TPR.G40697
                            [e_value] => 2.4e-09
                            [bit_score] => 67.4
                            [alignment_length] => 75
                            [identity_percentage] => 38.7
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0000218g0020] => Array
                        (
                            [gene_id] => Nitab4.5_0000218g0020
                            [e_value] => 3.2e-09
                            [bit_score] => 67.0
                            [alignment_length] => 73
                            [identity_percentage] => 43.8
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D009165
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.N4GRIJ] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.N4GRIJ
                            [e_value] => 4.2e-09
                            [bit_score] => 66.6
                            [alignment_length] => 34
                            [identity_percentage] => 94.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.RSIS5G] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.RSIS5G
                            [e_value] => 4.2e-09
                            [bit_score] => 66.6
                            [alignment_length] => 288
                            [identity_percentage] => 24.3
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.Y9BXYH] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.Y9BXYH
                            [e_value] => 4.2e-09
                            [bit_score] => 66.6
                            [alignment_length] => 86
                            [identity_percentage] => 39.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0016672] => Array
                        (
                            [gene_id] => Lj1g0016672
                            [e_value] => 5.4e-09
                            [bit_score] => 66.2
                            [alignment_length] => 52
                            [identity_percentage] => 55.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0004387] => Array
                        (
                            [gene_id] => Lj2g0004387
                            [e_value] => 5.4e-09
                            [bit_score] => 66.2
                            [alignment_length] => 52
                            [identity_percentage] => 55.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj4g0023280] => Array
                        (
                            [gene_id] => Lj4g0023280
                            [e_value] => 5.4e-09
                            [bit_score] => 66.2
                            [alignment_length] => 52
                            [identity_percentage] => 55.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C002890.2] => Array
                        (
                            [gene_id] => MELO3C002890.2
                            [e_value] => 7.1e-09
                            [bit_score] => 65.9
                            [alignment_length] => 98
                            [identity_percentage] => 30.6
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0001302g0040] => Array
                        (
                            [gene_id] => Nitab4.5_0001302g0040
                            [e_value] => 7.1e-09
                            [bit_score] => 65.9
                            [alignment_length] => 78
                            [identity_percentage] => 47.4
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D001850
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [Sopen12g012220] => Array
                        (
                            [gene_id] => Sopen12g012220
                            [e_value] => 7.1e-09
                            [bit_score] => 65.9
                            [alignment_length] => 96
                            [identity_percentage] => 36.5
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Atru.chr1.2247] => Array
                        (
                            [gene_id] => Atru.chr1.2247
                            [e_value] => 1.2e-08
                            [bit_score] => 65.1
                            [alignment_length] => 113
                            [identity_percentage] => 31.9
                            [species] => acertr
                            [common_name] => Acer truncatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C031980.2] => Array
                        (
                            [gene_id] => MELO3C031980.2
                            [e_value] => 1.2e-08
                            [bit_score] => 65.1
                            [alignment_length] => 93
                            [identity_percentage] => 33.3
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Hund20332] => Array
                        (
                            [gene_id] => Hund20332
                            [e_value] => 1.2e-08
                            [bit_score] => 65.1
                            [alignment_length] => 300
                            [identity_percentage] => 23.7
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D009844
                                )

                        )

                    [Lj2g0028079] => Array
                        (
                            [gene_id] => Lj2g0028079
                            [e_value] => 1.6e-08
                            [bit_score] => 64.7
                            [alignment_length] => 52
                            [identity_percentage] => 53.8
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0003085g0030] => Array
                        (
                            [gene_id] => Nitab4.5_0003085g0030
                            [e_value] => 2.1e-08
                            [bit_score] => 64.3
                            [alignment_length] => 77
                            [identity_percentage] => 45.5
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D009165
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [Sed0023676] => Array
                        (
                            [gene_id] => Sed0023676
                            [e_value] => 2.1e-08
                            [bit_score] => 64.3
                            [alignment_length] => 75
                            [identity_percentage] => 37.3
                            [species] => sed
                            [common_name] => Sechium edule
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Hund15556] => Array
                        (
                            [gene_id] => Hund15556
                            [e_value] => 2.1e-08
                            [bit_score] => 64.3
                            [alignment_length] => 298
                            [identity_percentage] => 23.8
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D009844
                                )

                        )

                    [Sopen01g009070] => Array
                        (
                            [gene_id] => Sopen01g009070
                            [e_value] => 2.1e-08
                            [bit_score] => 64.3
                            [alignment_length] => 69
                            [identity_percentage] => 43.5
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Glyma.01G130900] => Array
                        (
                            [gene_id] => Glyma.01G130900
                            [e_value] => 2.7e-08
                            [bit_score] => 63.9
                            [alignment_length] => 52
                            [identity_percentage] => 53.8
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [PGSC0003DMG400036915] => Array
                        (
                            [gene_id] => PGSC0003DMG400036915
                            [e_value] => 2.7e-08
                            [bit_score] => 63.9
                            [alignment_length] => 99
                            [identity_percentage] => 28.3
                            [species] => stu
                            [common_name] => Solanum tuberosum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Atru.chr4.268] => Array
                        (
                            [gene_id] => Atru.chr4.268
                            [e_value] => 3.5e-08
                            [bit_score] => 63.5
                            [alignment_length] => 113
                            [identity_percentage] => 31.0
                            [species] => acertr
                            [common_name] => Acer truncatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C030587.2] => Array
                        (
                            [gene_id] => MELO3C030587.2
                            [e_value] => 3.5e-08
                            [bit_score] => 63.5
                            [alignment_length] => 98
                            [identity_percentage] => 29.6
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Atru.chr1.207] => Array
                        (
                            [gene_id] => Atru.chr1.207
                            [e_value] => 4.6e-08
                            [bit_score] => 63.2
                            [alignment_length] => 262
                            [identity_percentage] => 24.4
                            [species] => acertr
                            [common_name] => Acer truncatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C027490.2] => Array
                        (
                            [gene_id] => MELO3C027490.2
                            [e_value] => 6.0e-08
                            [bit_score] => 62.8
                            [alignment_length] => 98
                            [identity_percentage] => 28.6
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj1g0005560] => Array
                        (
                            [gene_id] => Lj1g0005560
                            [e_value] => 6.0e-08
                            [bit_score] => 62.8
                            [alignment_length] => 50
                            [identity_percentage] => 56.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.M0U8W3] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M0U8W3
                            [e_value] => 7.9e-08
                            [bit_score] => 62.4
                            [alignment_length] => 31
                            [identity_percentage] => 93.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0010792] => Array
                        (
                            [gene_id] => Lj2g0010792
                            [e_value] => 7.9e-08
                            [bit_score] => 62.4
                            [alignment_length] => 50
                            [identity_percentage] => 56.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0026449] => Array
                        (
                            [gene_id] => Lj2g0026449
                            [e_value] => 7.9e-08
                            [bit_score] => 62.4
                            [alignment_length] => 50
                            [identity_percentage] => 54.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj3g0011191] => Array
                        (
                            [gene_id] => Lj3g0011191
                            [e_value] => 7.9e-08
                            [bit_score] => 62.4
                            [alignment_length] => 50
                            [identity_percentage] => 54.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj4g0027308] => Array
                        (
                            [gene_id] => Lj4g0027308
                            [e_value] => 7.9e-08
                            [bit_score] => 62.4
                            [alignment_length] => 50
                            [identity_percentage] => 54.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj6g0006038] => Array
                        (
                            [gene_id] => Lj6g0006038
                            [e_value] => 7.9e-08
                            [bit_score] => 62.4
                            [alignment_length] => 50
                            [identity_percentage] => 54.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen09g015100] => Array
                        (
                            [gene_id] => Sopen09g015100
                            [e_value] => 1.0e-07
                            [bit_score] => 62.0
                            [alignment_length] => 71
                            [identity_percentage] => 42.3
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen11g007840] => Array
                        (
                            [gene_id] => Sopen11g007840
                            [e_value] => 1.0e-07
                            [bit_score] => 62.0
                            [alignment_length] => 75
                            [identity_percentage] => 38.7
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen10g016530] => Array
                        (
                            [gene_id] => Sopen10g016530
                            [e_value] => 1.3e-07
                            [bit_score] => 61.6
                            [alignment_length] => 75
                            [identity_percentage] => 38.7
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.VAKC15] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.VAKC15
                            [e_value] => 1.8e-07
                            [bit_score] => 61.2
                            [alignment_length] => 233
                            [identity_percentage] => 25.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [CiPaw.02G081200] => Array
                        (
                            [gene_id] => CiPaw.02G081200
                            [e_value] => 1.8e-07
                            [bit_score] => 61.2
                            [alignment_length] => 59
                            [identity_percentage] => 47.5
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Lj2g0026023] => Array
                        (
                            [gene_id] => Lj2g0026023
                            [e_value] => 1.8e-07
                            [bit_score] => 61.2
                            [alignment_length] => 50
                            [identity_percentage] => 52.0
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu050619.1] => Array
                        (
                            [gene_id] => Oeu050619.1
                            [e_value] => 1.8e-07
                            [bit_score] => 61.2
                            [alignment_length] => 85
                            [identity_percentage] => 37.6
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D004680
                                    [ORTHOFAM] => ORTHO05D005939
                                )

                        )

                    [CAN.G150.7] => Array
                        (
                            [gene_id] => CAN.G150.7
                            [e_value] => 2.3e-07
                            [bit_score] => 60.8
                            [alignment_length] => 71
                            [identity_percentage] => 43.7
                            [species] => can
                            [common_name] => Capsicum annuum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.X91M1R] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.X91M1R
                            [e_value] => 3.0e-07
                            [bit_score] => 60.5
                            [alignment_length] => 79
                            [identity_percentage] => 43.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen01g025440] => Array
                        (
                            [gene_id] => Sopen01g025440
                            [e_value] => 3.9e-07
                            [bit_score] => 60.1
                            [alignment_length] => 75
                            [identity_percentage] => 40.0
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen09g015140] => Array
                        (
                            [gene_id] => Sopen09g015140
                            [e_value] => 3.9e-07
                            [bit_score] => 60.1
                            [alignment_length] => 91
                            [identity_percentage] => 35.2
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen05g019960] => Array
                        (
                            [gene_id] => Sopen05g019960
                            [e_value] => 5.1e-07
                            [bit_score] => 59.7
                            [alignment_length] => 75
                            [identity_percentage] => 40.0
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen09g015650] => Array
                        (
                            [gene_id] => Sopen09g015650
                            [e_value] => 5.1e-07
                            [bit_score] => 59.7
                            [alignment_length] => 75
                            [identity_percentage] => 37.3
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.EDY1F1] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.EDY1F1
                            [e_value] => 6.7e-07
                            [bit_score] => 59.3
                            [alignment_length] => 131
                            [identity_percentage] => 27.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Oeu064487.1] => Array
                        (
                            [gene_id] => Oeu064487.1
                            [e_value] => 6.7e-07
                            [bit_score] => 59.3
                            [alignment_length] => 248
                            [identity_percentage] => 27.4
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D010634
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.AYPR9V] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.AYPR9V
                            [e_value] => 8.7e-07
                            [bit_score] => 58.9
                            [alignment_length] => 95
                            [identity_percentage] => 35.8
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.SIP0JR] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.SIP0JR
                            [e_value] => 8.7e-07
                            [bit_score] => 58.9
                            [alignment_length] => 78
                            [identity_percentage] => 41.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C030509.2] => Array
                        (
                            [gene_id] => MELO3C030509.2
                            [e_value] => 1.1e-06
                            [bit_score] => 58.5
                            [alignment_length] => 168
                            [identity_percentage] => 27.4
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D015087
                                )

                        )

                    [Manes.10G066150] => Array
                        (
                            [gene_id] => Manes.10G066150
                            [e_value] => 1.1e-06
                            [bit_score] => 58.5
                            [alignment_length] => 52
                            [identity_percentage] => 46.2
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0000274g0170] => Array
                        (
                            [gene_id] => Nitab4.5_0000274g0170
                            [e_value] => 1.1e-06
                            [bit_score] => 58.5
                            [alignment_length] => 78
                            [identity_percentage] => 41.0
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D009165
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [Sopen05g024500] => Array
                        (
                            [gene_id] => Sopen05g024500
                            [e_value] => 1.1e-06
                            [bit_score] => 58.5
                            [alignment_length] => 75
                            [identity_percentage] => 37.3
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.M6QS4E] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.M6QS4E
                            [e_value] => 1.5e-06
                            [bit_score] => 58.2
                            [alignment_length] => 254
                            [identity_percentage] => 23.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.XV275J] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.XV275J
                            [e_value] => 1.5e-06
                            [bit_score] => 58.2
                            [alignment_length] => 131
                            [identity_percentage] => 27.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Thhalv10022480m.g] => Array
                        (
                            [gene_id] => Thhalv10022480m.g
                            [e_value] => 1.5e-06
                            [bit_score] => 58.2
                            [alignment_length] => 104
                            [identity_percentage] => 30.8
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen11g016660] => Array
                        (
                            [gene_id] => Sopen11g016660
                            [e_value] => 1.5e-06
                            [bit_score] => 58.2
                            [alignment_length] => 130
                            [identity_percentage] => 30.0
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen12g012480] => Array
                        (
                            [gene_id] => Sopen12g012480
                            [e_value] => 1.9e-06
                            [bit_score] => 57.8
                            [alignment_length] => 75
                            [identity_percentage] => 37.3
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0003796g0110] => Array
                        (
                            [gene_id] => Nitab4.5_0003796g0110
                            [e_value] => 2.5e-06
                            [bit_score] => 57.4
                            [alignment_length] => 81
                            [identity_percentage] => 39.5
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D009165
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [Sopen03g014160] => Array
                        (
                            [gene_id] => Sopen03g014160
                            [e_value] => 2.5e-06
                            [bit_score] => 57.4
                            [alignment_length] => 75
                            [identity_percentage] => 38.7
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000004
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Sopen11g007830] => Array
                        (
                            [gene_id] => Sopen11g007830
                            [e_value] => 4.3e-06
                            [bit_score] => 56.6
                            [alignment_length] => 75
                            [identity_percentage] => 37.3
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [MELO3C026406.2] => Array
                        (
                            [gene_id] => MELO3C026406.2
                            [e_value] => 5.6e-06
                            [bit_score] => 56.2
                            [alignment_length] => 266
                            [identity_percentage] => 22.9
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0008503g0020] => Array
                        (
                            [gene_id] => Nitab4.5_0008503g0020
                            [e_value] => 5.6e-06
                            [bit_score] => 56.2
                            [alignment_length] => 81
                            [identity_percentage] => 38.3
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D009165
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.C5B7DM] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.C5B7DM
                            [e_value] => 7.4e-06
                            [bit_score] => 55.8
                            [alignment_length] => 84
                            [identity_percentage] => 45.2
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.SI7STU] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.SI7STU
                            [e_value] => 7.4e-06
                            [bit_score] => 55.8
                            [alignment_length] => 38
                            [identity_percentage] => 73.7
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.X0U8Y0] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.X0U8Y0
                            [e_value] => 7.4e-06
                            [bit_score] => 55.8
                            [alignment_length] => 53
                            [identity_percentage] => 49.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D000158
                                    [ORTHOFAM] => ORTHO05D000197
                                )

                        )

                    [Nitab4.5_0000125g0390] => Array
                        (
                            [gene_id] => Nitab4.5_0000125g0390
                            [e_value] => 9.6e-06
                            [bit_score] => 55.5
                            [alignment_length] => 72
                            [identity_percentage] => 45.8
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D009165
                                    [ORTHOFAM] => ORTHO05D011118
                                )

                        )

                )

            [similarity_hits_species] => Array
                (
                    [arhy] => Array
                        (
                            [0] => arahy.Tifrunner.gnm1.ann1.87PAU8
                            [1] => arahy.Tifrunner.gnm1.ann1.GW23Z6
                            [2] => arahy.Tifrunner.gnm1.ann1.T41GG2
                            [3] => arahy.Tifrunner.gnm1.ann1.625I4R
                            [4] => arahy.Tifrunner.gnm1.ann1.LDA4IK
                            [5] => arahy.Tifrunner.gnm1.ann1.3AR30J
                            [6] => arahy.Tifrunner.gnm1.ann1.ZY293U
                            [7] => arahy.Tifrunner.gnm1.ann1.9T44NN
                            [8] => arahy.Tifrunner.gnm1.ann1.JB5G6S
                            [9] => arahy.Tifrunner.gnm1.ann1.4R1N6H
                            [10] => arahy.Tifrunner.gnm1.ann1.7UIB1D
                            [11] => arahy.Tifrunner.gnm1.ann1.390B12
                            [12] => arahy.Tifrunner.gnm1.ann1.HIWB5S
                            [13] => arahy.Tifrunner.gnm1.ann1.86RVGQ
                            [14] => arahy.Tifrunner.gnm1.ann1.HQL5ZH
                            [15] => arahy.Tifrunner.gnm1.ann1.44H41D
                            [16] => arahy.Tifrunner.gnm1.ann1.NZ73MH
                            [17] => arahy.Tifrunner.gnm1.ann1.PTE4RY
                            [18] => arahy.Tifrunner.gnm1.ann1.TLT0RJ
                            [19] => arahy.Tifrunner.gnm1.ann1.19B2C5
                            [20] => arahy.Tifrunner.gnm1.ann1.DX7X9L
                            [21] => arahy.Tifrunner.gnm1.ann1.VG5MUL
                            [22] => arahy.Tifrunner.gnm1.ann1.YKB7VN
                            [23] => arahy.Tifrunner.gnm1.ann1.K985UN
                            [24] => arahy.Tifrunner.gnm1.ann1.T3114H
                            [25] => arahy.Tifrunner.gnm1.ann1.0FE5EB
                            [26] => arahy.Tifrunner.gnm1.ann1.22A0BZ
                            [27] => arahy.Tifrunner.gnm1.ann1.G16GBW
                            [28] => arahy.Tifrunner.gnm1.ann1.DILN7M
                            [29] => arahy.Tifrunner.gnm1.ann1.MF1Z11
                            [30] => arahy.Tifrunner.gnm1.ann1.N38U72
                            [31] => arahy.Tifrunner.gnm1.ann1.67AQV3
                            [32] => arahy.Tifrunner.gnm1.ann1.EDB0QK
                            [33] => arahy.Tifrunner.gnm1.ann1.HWFE7W
                            [34] => arahy.Tifrunner.gnm1.ann1.8U8QG7
                            [35] => arahy.Tifrunner.gnm1.ann1.PC9UR1
                            [36] => arahy.Tifrunner.gnm1.ann1.618FAS
                            [37] => arahy.Tifrunner.gnm1.ann1.Y4MBR7
                            [38] => arahy.Tifrunner.gnm1.ann1.KB372Z
                            [39] => arahy.Tifrunner.gnm1.ann1.X8XTSC
                            [40] => arahy.Tifrunner.gnm1.ann1.ZU9EK6
                            [41] => arahy.Tifrunner.gnm1.ann1.G6BTHS
                            [42] => arahy.Tifrunner.gnm1.ann1.XF3T5B
                            [43] => arahy.Tifrunner.gnm1.ann1.JSYE9A
                            [44] => arahy.Tifrunner.gnm1.ann1.L849KL
                            [45] => arahy.Tifrunner.gnm1.ann1.LIE4DR
                            [46] => arahy.Tifrunner.gnm1.ann1.5U1Y5S
                            [47] => arahy.Tifrunner.gnm1.ann1.BCFP52
                            [48] => arahy.Tifrunner.gnm1.ann1.AX1X9T
                            [49] => arahy.Tifrunner.gnm1.ann1.F7WSSH
                            [50] => arahy.Tifrunner.gnm1.ann1.P91A7Q
                            [51] => arahy.Tifrunner.gnm1.ann1.3DW5CS
                            [52] => arahy.Tifrunner.gnm1.ann1.P60MR3
                            [53] => arahy.Tifrunner.gnm1.ann1.Q47VXP
                            [54] => arahy.Tifrunner.gnm1.ann1.A109Z1
                            [55] => arahy.Tifrunner.gnm1.ann1.580H8T
                            [56] => arahy.Tifrunner.gnm1.ann1.YCB991
                            [57] => arahy.Tifrunner.gnm1.ann1.1VG8AV
                            [58] => arahy.Tifrunner.gnm1.ann1.RM1BJK
                            [59] => arahy.Tifrunner.gnm1.ann1.VSM9EK
                            [60] => arahy.Tifrunner.gnm1.ann1.BY1LZF
                            [61] => arahy.Tifrunner.gnm1.ann1.1J5WG7
                            [62] => arahy.Tifrunner.gnm1.ann1.ICE72P
                            [63] => arahy.Tifrunner.gnm1.ann1.M3XE2W
                            [64] => arahy.Tifrunner.gnm1.ann1.YH0HYY
                            [65] => arahy.Tifrunner.gnm1.ann1.3413VH
                            [66] => arahy.Tifrunner.gnm1.ann1.PDU7VZ
                            [67] => arahy.Tifrunner.gnm1.ann1.Y3RU0I
                            [68] => arahy.Tifrunner.gnm1.ann1.X7WWLG
                            [69] => arahy.Tifrunner.gnm1.ann1.D3KQFI
                            [70] => arahy.Tifrunner.gnm1.ann1.UN49J0
                            [71] => arahy.Tifrunner.gnm1.ann1.79H2ZA
                            [72] => arahy.Tifrunner.gnm1.ann1.M915JV
                            [73] => arahy.Tifrunner.gnm1.ann1.IUFC7V
                            [74] => arahy.Tifrunner.gnm1.ann1.3TU4M5
                            [75] => arahy.Tifrunner.gnm1.ann1.7580UM
                            [76] => arahy.Tifrunner.gnm1.ann1.UCKJ4P
                            [77] => arahy.Tifrunner.gnm1.ann1.BW0SGT
                            [78] => arahy.Tifrunner.gnm1.ann1.U0J92L
                            [79] => arahy.Tifrunner.gnm1.ann1.0I80A4
                            [80] => arahy.Tifrunner.gnm1.ann1.5KY2TX
                            [81] => arahy.Tifrunner.gnm1.ann1.ITS72S
                            [82] => arahy.Tifrunner.gnm1.ann1.HM98QR
                            [83] => arahy.Tifrunner.gnm1.ann1.NVTW2S
                            [84] => arahy.Tifrunner.gnm1.ann1.P2IVNE
                            [85] => arahy.Tifrunner.gnm1.ann1.DZ8CJX
                            [86] => arahy.Tifrunner.gnm1.ann1.WU79S3
                            [87] => arahy.Tifrunner.gnm1.ann1.K76VAT
                            [88] => arahy.Tifrunner.gnm1.ann1.LT085V
                            [89] => arahy.Tifrunner.gnm1.ann1.1ZE7SC
                            [90] => arahy.Tifrunner.gnm1.ann1.RVWB0M
                            [91] => arahy.Tifrunner.gnm1.ann1.FG7H5S
                            [92] => arahy.Tifrunner.gnm1.ann1.QYWZ0N
                            [93] => arahy.Tifrunner.gnm1.ann1.MI8TNQ
                            [94] => arahy.Tifrunner.gnm1.ann1.CQ5GAN
                            [95] => arahy.Tifrunner.gnm1.ann1.FX7YCE
                            [96] => arahy.Tifrunner.gnm1.ann1.QFB33Z
                            [97] => arahy.Tifrunner.gnm1.ann1.AVU11B
                            [98] => arahy.Tifrunner.gnm1.ann1.YM3WRX
                            [99] => arahy.Tifrunner.gnm1.ann1.AXU1GU
                            [100] => arahy.Tifrunner.gnm1.ann1.VHLD2J
                            [101] => arahy.Tifrunner.gnm1.ann1.EVFR00
                            [102] => arahy.Tifrunner.gnm1.ann1.DBEW1J
                            [103] => arahy.Tifrunner.gnm1.ann1.DUA4ZE
                            [104] => arahy.Tifrunner.gnm1.ann1.Q9UUMB
                            [105] => arahy.Tifrunner.gnm1.ann1.217P67
                            [106] => arahy.Tifrunner.gnm1.ann1.SPE56M
                            [107] => arahy.Tifrunner.gnm1.ann1.YRHH3L
                            [108] => arahy.Tifrunner.gnm1.ann1.IE1D11
                            [109] => arahy.Tifrunner.gnm1.ann1.6U6G8M
                            [110] => arahy.Tifrunner.gnm1.ann1.C593YE
                            [111] => arahy.Tifrunner.gnm1.ann1.31ESZ9
                            [112] => arahy.Tifrunner.gnm1.ann1.UQ4A0Q
                            [113] => arahy.Tifrunner.gnm1.ann1.FHGQ5B
                            [114] => arahy.Tifrunner.gnm1.ann1.AR04AZ
                            [115] => arahy.Tifrunner.gnm1.ann1.6I2GPK
                            [116] => arahy.Tifrunner.gnm1.ann1.B6EIU5
                            [117] => arahy.Tifrunner.gnm1.ann1.2708NW
                            [118] => arahy.Tifrunner.gnm1.ann1.35BD43
                            [119] => arahy.Tifrunner.gnm1.ann1.3EDM9V
                            [120] => arahy.Tifrunner.gnm1.ann1.XJX9BL
                            [121] => arahy.Tifrunner.gnm1.ann1.62B9ZV
                            [122] => arahy.Tifrunner.gnm1.ann1.H6F6PF
                            [123] => arahy.Tifrunner.gnm1.ann1.UNC6RI
                            [124] => arahy.Tifrunner.gnm1.ann1.EXLZ0E
                            [125] => arahy.Tifrunner.gnm1.ann1.QGN7FK
                            [126] => arahy.Tifrunner.gnm1.ann1.AQ8SFL
                            [127] => arahy.Tifrunner.gnm1.ann1.99ZMK7
                            [128] => arahy.Tifrunner.gnm1.ann1.YPZK8G
                            [129] => arahy.Tifrunner.gnm1.ann1.EA1KS6
                            [130] => arahy.Tifrunner.gnm1.ann1.PNX89E
                            [131] => arahy.Tifrunner.gnm1.ann1.1H3RP1
                            [132] => arahy.Tifrunner.gnm1.ann1.QV8Q6T
                            [133] => arahy.Tifrunner.gnm1.ann1.SSLH32
                            [134] => arahy.Tifrunner.gnm1.ann1.Y0F1XT
                            [135] => arahy.Tifrunner.gnm1.ann1.4GS65V
                            [136] => arahy.Tifrunner.gnm1.ann1.D940DF
                            [137] => arahy.Tifrunner.gnm1.ann1.FK4Q8T
                            [138] => arahy.Tifrunner.gnm1.ann1.4TEP00
                            [139] => arahy.Tifrunner.gnm1.ann1.ZD1FV2
                            [140] => arahy.Tifrunner.gnm1.ann1.I0MGU7
                            [141] => arahy.Tifrunner.gnm1.ann1.RTS1QS
                            [142] => arahy.Tifrunner.gnm1.ann1.96FB1P
                            [143] => arahy.Tifrunner.gnm1.ann1.D12JGJ
                            [144] => arahy.Tifrunner.gnm1.ann1.I4SF0Q
                            [145] => arahy.Tifrunner.gnm1.ann1.Z0B08L
                            [146] => arahy.Tifrunner.gnm1.ann1.VE75MW
                            [147] => arahy.Tifrunner.gnm1.ann1.Q6JBKT
                            [148] => arahy.Tifrunner.gnm1.ann1.J30PZF
                            [149] => arahy.Tifrunner.gnm1.ann1.35SW51
                            [150] => arahy.Tifrunner.gnm1.ann1.FC8ITA
                            [151] => arahy.Tifrunner.gnm1.ann1.9VH52Z
                            [152] => arahy.Tifrunner.gnm1.ann1.CDRG1U
                            [153] => arahy.Tifrunner.gnm1.ann1.Q7RZT9
                            [154] => arahy.Tifrunner.gnm1.ann1.X2BPFT
                            [155] => arahy.Tifrunner.gnm1.ann1.YN5V9H
                            [156] => arahy.Tifrunner.gnm1.ann1.B2TA0B
                            [157] => arahy.Tifrunner.gnm1.ann1.89MAKE
                            [158] => arahy.Tifrunner.gnm1.ann1.Z01BNV
                            [159] => arahy.Tifrunner.gnm1.ann1.DWAY4T
                            [160] => arahy.Tifrunner.gnm1.ann1.RC9HZP
                            [161] => arahy.Tifrunner.gnm1.ann1.N3KJBP
                            [162] => arahy.Tifrunner.gnm1.ann1.FFB5CH
                            [163] => arahy.Tifrunner.gnm1.ann1.219KTT
                            [164] => arahy.Tifrunner.gnm1.ann1.KH03IP
                            [165] => arahy.Tifrunner.gnm1.ann1.HQ7VS1
                            [166] => arahy.Tifrunner.gnm1.ann1.VX28TM
                            [167] => arahy.Tifrunner.gnm1.ann1.6A4TC1
                            [168] => arahy.Tifrunner.gnm1.ann1.N9660C
                            [169] => arahy.Tifrunner.gnm1.ann1.IPE5VY
                            [170] => arahy.Tifrunner.gnm1.ann1.BG80MW
                            [171] => arahy.Tifrunner.gnm1.ann1.XS5DYX
                            [172] => arahy.Tifrunner.gnm1.ann1.IRD4WN
                            [173] => arahy.Tifrunner.gnm1.ann1.6TZ82I
                            [174] => arahy.Tifrunner.gnm1.ann1.Z8R2P5
                            [175] => arahy.Tifrunner.gnm1.ann1.HZWW81
                            [176] => arahy.Tifrunner.gnm1.ann1.MRFE53
                            [177] => arahy.Tifrunner.gnm1.ann1.M3JTMX
                            [178] => arahy.Tifrunner.gnm1.ann1.6D93L5
                            [179] => arahy.Tifrunner.gnm1.ann1.E2IS3L
                            [180] => arahy.Tifrunner.gnm1.ann1.9BX371
                            [181] => arahy.Tifrunner.gnm1.ann1.A3328F
                            [182] => arahy.Tifrunner.gnm1.ann1.54H83L
                            [183] => arahy.Tifrunner.gnm1.ann1.T3KCYU
                            [184] => arahy.Tifrunner.gnm1.ann1.Y4Y8ET
                            [185] => arahy.Tifrunner.gnm1.ann1.IA7WGU
                            [186] => arahy.Tifrunner.gnm1.ann1.APK0NP
                            [187] => arahy.Tifrunner.gnm1.ann1.2SA9QW
                            [188] => arahy.Tifrunner.gnm1.ann1.3L2L0Y
                            [189] => arahy.Tifrunner.gnm1.ann1.2EH0QW
                            [190] => arahy.Tifrunner.gnm1.ann1.CLW9FC
                            [191] => arahy.Tifrunner.gnm1.ann1.QI581D
                            [192] => arahy.Tifrunner.gnm1.ann1.U4M58P
                            [193] => arahy.Tifrunner.gnm1.ann1.0G7P3D
                            [194] => arahy.Tifrunner.gnm1.ann1.HB2SP5
                            [195] => arahy.Tifrunner.gnm1.ann1.0UKE70
                            [196] => arahy.Tifrunner.gnm1.ann1.WSML5L
                            [197] => arahy.Tifrunner.gnm1.ann1.71573I
                            [198] => arahy.Tifrunner.gnm1.ann1.0G5FLV
                            [199] => arahy.Tifrunner.gnm1.ann1.IQR40G
                            [200] => arahy.Tifrunner.gnm1.ann1.C99TYC
                            [201] => arahy.Tifrunner.gnm1.ann1.F0AUH3
                            [202] => arahy.Tifrunner.gnm1.ann1.90XE5V
                            [203] => arahy.Tifrunner.gnm1.ann1.QD41U6
                            [204] => arahy.Tifrunner.gnm1.ann1.G2V00H
                            [205] => arahy.Tifrunner.gnm1.ann1.Q6MQNA
                            [206] => arahy.Tifrunner.gnm1.ann1.KU6KXV
                            [207] => arahy.Tifrunner.gnm1.ann1.R7CRBK
                            [208] => arahy.Tifrunner.gnm1.ann1.JFJ878
                            [209] => arahy.Tifrunner.gnm1.ann1.K0EZJ4
                            [210] => arahy.Tifrunner.gnm1.ann1.659L4B
                            [211] => arahy.Tifrunner.gnm1.ann1.AV92MX
                            [212] => arahy.Tifrunner.gnm1.ann1.VHU47D
                            [213] => arahy.Tifrunner.gnm1.ann1.JNB467
                            [214] => arahy.Tifrunner.gnm1.ann1.XN6NS8
                            [215] => arahy.Tifrunner.gnm1.ann1.1P3WRE
                            [216] => arahy.Tifrunner.gnm1.ann1.W04P42
                            [217] => arahy.Tifrunner.gnm1.ann1.Y1KF2B
                            [218] => arahy.Tifrunner.gnm1.ann1.BEX5HG
                            [219] => arahy.Tifrunner.gnm1.ann1.Q72NH6
                            [220] => arahy.Tifrunner.gnm1.ann1.S1Q5XH
                            [221] => arahy.Tifrunner.gnm1.ann1.18PYUZ
                            [222] => arahy.Tifrunner.gnm1.ann1.8K0ZU0
                            [223] => arahy.Tifrunner.gnm1.ann1.I3DMP8
                            [224] => arahy.Tifrunner.gnm1.ann1.9Y4FQ2
                            [225] => arahy.Tifrunner.gnm1.ann1.I7E4L8
                            [226] => arahy.Tifrunner.gnm1.ann1.IW28EF
                            [227] => arahy.Tifrunner.gnm1.ann1.GD7WFM
                            [228] => arahy.Tifrunner.gnm1.ann1.N3555V
                            [229] => arahy.Tifrunner.gnm1.ann1.QGF57N
                            [230] => arahy.Tifrunner.gnm1.ann1.V0BAMU
                            [231] => arahy.Tifrunner.gnm1.ann1.72MBZZ
                            [232] => arahy.Tifrunner.gnm1.ann1.756TEX
                            [233] => arahy.Tifrunner.gnm1.ann1.HTN0Y5
                            [234] => arahy.Tifrunner.gnm1.ann1.ZZQG32
                            [235] => arahy.Tifrunner.gnm1.ann1.4EM99Z
                            [236] => arahy.Tifrunner.gnm1.ann1.CX12M5
                            [237] => arahy.Tifrunner.gnm1.ann1.N7R8CX
                            [238] => arahy.Tifrunner.gnm1.ann1.YL2BBV
                            [239] => arahy.Tifrunner.gnm1.ann1.39JP8F
                            [240] => arahy.Tifrunner.gnm1.ann1.5S8HU1
                            [241] => arahy.Tifrunner.gnm1.ann1.6U09DB
                            [242] => arahy.Tifrunner.gnm1.ann1.CIR6XW
                            [243] => arahy.Tifrunner.gnm1.ann1.FHI9NT
                            [244] => arahy.Tifrunner.gnm1.ann1.JCQ008
                            [245] => arahy.Tifrunner.gnm1.ann1.7I5EIZ
                            [246] => arahy.Tifrunner.gnm1.ann1.CVS9SJ
                            [247] => arahy.Tifrunner.gnm1.ann1.HEVL9E
                            [248] => arahy.Tifrunner.gnm1.ann1.M97NZA
                            [249] => arahy.Tifrunner.gnm1.ann1.BYBE5B
                            [250] => arahy.Tifrunner.gnm1.ann1.I3V9I7
                            [251] => arahy.Tifrunner.gnm1.ann1.J01ZYU
                            [252] => arahy.Tifrunner.gnm1.ann1.TA1UNZ
                            [253] => arahy.Tifrunner.gnm1.ann1.4JGR2S
                            [254] => arahy.Tifrunner.gnm1.ann1.M9M3R0
                            [255] => arahy.Tifrunner.gnm1.ann1.RZIJ2L
                            [256] => arahy.Tifrunner.gnm1.ann1.ZPS03P
                            [257] => arahy.Tifrunner.gnm1.ann1.EUAW6M
                            [258] => arahy.Tifrunner.gnm1.ann1.GIY5N5
                            [259] => arahy.Tifrunner.gnm1.ann1.UC4KU4
                            [260] => arahy.Tifrunner.gnm1.ann1.ZIM2T0
                            [261] => arahy.Tifrunner.gnm1.ann1.9F14AA
                            [262] => arahy.Tifrunner.gnm1.ann1.EKYZ7W
                            [263] => arahy.Tifrunner.gnm1.ann1.GCX1C5
                            [264] => arahy.Tifrunner.gnm1.ann1.GJ1AII
                            [265] => arahy.Tifrunner.gnm1.ann1.HUSQ38
                            [266] => arahy.Tifrunner.gnm1.ann1.QV2FY5
                            [267] => arahy.Tifrunner.gnm1.ann1.SEYZ0I
                            [268] => arahy.Tifrunner.gnm1.ann1.3V14JX
                            [269] => arahy.Tifrunner.gnm1.ann1.IUXR99
                            [270] => arahy.Tifrunner.gnm1.ann1.NT2WSK
                            [271] => arahy.Tifrunner.gnm1.ann1.M2MFDB
                            [272] => arahy.Tifrunner.gnm1.ann1.NF0PPL
                            [273] => arahy.Tifrunner.gnm1.ann1.C39H2M
                            [274] => arahy.Tifrunner.gnm1.ann1.JP535L
                            [275] => arahy.Tifrunner.gnm1.ann1.DQ3ZQE
                            [276] => arahy.Tifrunner.gnm1.ann1.ZMN0FL
                            [277] => arahy.Tifrunner.gnm1.ann1.68U12A
                            [278] => arahy.Tifrunner.gnm1.ann1.PYBE03
                            [279] => arahy.Tifrunner.gnm1.ann1.Z93FG5
                            [280] => arahy.Tifrunner.gnm1.ann1.W4MS58
                            [281] => arahy.Tifrunner.gnm1.ann1.2H9LFQ
                            [282] => arahy.Tifrunner.gnm1.ann1.8C5ZBV
                            [283] => arahy.Tifrunner.gnm1.ann1.T6DPWG
                            [284] => arahy.Tifrunner.gnm1.ann1.V4TPZ0
                            [285] => arahy.Tifrunner.gnm1.ann1.8UCL89
                            [286] => arahy.Tifrunner.gnm1.ann1.848KF4
                            [287] => arahy.Tifrunner.gnm1.ann1.9363QZ
                            [288] => arahy.Tifrunner.gnm1.ann1.Q2DA23
                            [289] => arahy.Tifrunner.gnm1.ann1.6F2NI6
                            [290] => arahy.Tifrunner.gnm1.ann1.P57W7I
                            [291] => arahy.Tifrunner.gnm1.ann1.9IG2T4
                            [292] => arahy.Tifrunner.gnm1.ann1.LSKZ83
                            [293] => arahy.Tifrunner.gnm1.ann1.N3AN7R
                            [294] => arahy.Tifrunner.gnm1.ann1.PGH66G
                            [295] => arahy.Tifrunner.gnm1.ann1.S13B92
                            [296] => arahy.Tifrunner.gnm1.ann1.WB5STR
                            [297] => arahy.Tifrunner.gnm1.ann1.UNLN87
                            [298] => arahy.Tifrunner.gnm1.ann1.Q4LR9P
                            [299] => arahy.Tifrunner.gnm1.ann1.0VPI4Y
                            [300] => arahy.Tifrunner.gnm1.ann1.0IRR4S
                            [301] => arahy.Tifrunner.gnm1.ann1.I58UVB
                            [302] => arahy.Tifrunner.gnm1.ann1.14KCD6
                            [303] => arahy.Tifrunner.gnm1.ann1.KK5I4J
                            [304] => arahy.Tifrunner.gnm1.ann1.45JVR9
                            [305] => arahy.Tifrunner.gnm1.ann1.7A5GZE
                            [306] => arahy.Tifrunner.gnm1.ann1.1RY5L5
                            [307] => arahy.Tifrunner.gnm1.ann1.558G8J
                            [308] => arahy.Tifrunner.gnm1.ann1.A5BTLM
                            [309] => arahy.Tifrunner.gnm1.ann1.IM0SRD
                            [310] => arahy.Tifrunner.gnm1.ann1.GI390R
                            [311] => arahy.Tifrunner.gnm1.ann1.H8F1EK
                            [312] => arahy.Tifrunner.gnm1.ann1.96HYEI
                            [313] => arahy.Tifrunner.gnm1.ann1.KY4VPW
                            [314] => arahy.Tifrunner.gnm1.ann1.WI178G
                            [315] => arahy.Tifrunner.gnm1.ann1.MH5L6C
                            [316] => arahy.Tifrunner.gnm1.ann1.C9QDYM
                            [317] => arahy.Tifrunner.gnm1.ann1.GQ521E
                            [318] => arahy.Tifrunner.gnm1.ann1.PC7CW8
                            [319] => arahy.Tifrunner.gnm1.ann1.8102HM
                            [320] => arahy.Tifrunner.gnm1.ann1.BYA8HJ
                            [321] => arahy.Tifrunner.gnm1.ann1.97NBY2
                            [322] => arahy.Tifrunner.gnm1.ann1.M3KMZQ
                            [323] => arahy.Tifrunner.gnm1.ann1.V7R3VA
                            [324] => arahy.Tifrunner.gnm1.ann1.CI6B6W
                            [325] => arahy.Tifrunner.gnm1.ann1.THNS6P
                            [326] => arahy.Tifrunner.gnm1.ann1.1Y1G78
                            [327] => arahy.Tifrunner.gnm1.ann1.IJ0KFI
                            [328] => arahy.Tifrunner.gnm1.ann1.ASBC4P
                            [329] => arahy.Tifrunner.gnm1.ann1.QZ4HHM
                            [330] => arahy.Tifrunner.gnm1.ann1.Y9U40M
                            [331] => arahy.Tifrunner.gnm1.ann1.Y76A0X
                            [332] => arahy.Tifrunner.gnm1.ann1.QJ2VLW
                            [333] => arahy.Tifrunner.gnm1.ann1.7FSK73
                            [334] => arahy.Tifrunner.gnm1.ann1.QJW6VR
                            [335] => arahy.Tifrunner.gnm1.ann1.65T66L
                            [336] => arahy.Tifrunner.gnm1.ann1.Q40EC9
                            [337] => arahy.Tifrunner.gnm1.ann1.T0AVIE
                            [338] => arahy.Tifrunner.gnm1.ann1.53R2A7
                            [339] => arahy.Tifrunner.gnm1.ann1.I9EK5P
                            [340] => arahy.Tifrunner.gnm1.ann1.DFQR10
                            [341] => arahy.Tifrunner.gnm1.ann1.82YQT6
                            [342] => arahy.Tifrunner.gnm1.ann1.4E97LE
                            [343] => arahy.Tifrunner.gnm1.ann1.1S4DUK
                            [344] => arahy.Tifrunner.gnm1.ann1.MZPE9F
                            [345] => arahy.Tifrunner.gnm1.ann1.S1M30Y
                            [346] => arahy.Tifrunner.gnm1.ann1.P29BXD
                            [347] => arahy.Tifrunner.gnm1.ann1.ZV0DC7
                            [348] => arahy.Tifrunner.gnm1.ann1.MQQ5HT
                            [349] => arahy.Tifrunner.gnm1.ann1.Y1GSKA
                            [350] => arahy.Tifrunner.gnm1.ann1.N4GRIJ
                            [351] => arahy.Tifrunner.gnm1.ann1.RSIS5G
                            [352] => arahy.Tifrunner.gnm1.ann1.Y9BXYH
                            [353] => arahy.Tifrunner.gnm1.ann1.M0U8W3
                            [354] => arahy.Tifrunner.gnm1.ann1.VAKC15
                            [355] => arahy.Tifrunner.gnm1.ann1.X91M1R
                            [356] => arahy.Tifrunner.gnm1.ann1.EDY1F1
                            [357] => arahy.Tifrunner.gnm1.ann1.AYPR9V
                            [358] => arahy.Tifrunner.gnm1.ann1.SIP0JR
                            [359] => arahy.Tifrunner.gnm1.ann1.M6QS4E
                            [360] => arahy.Tifrunner.gnm1.ann1.XV275J
                            [361] => arahy.Tifrunner.gnm1.ann1.C5B7DM
                            [362] => arahy.Tifrunner.gnm1.ann1.SI7STU
                            [363] => arahy.Tifrunner.gnm1.ann1.X0U8Y0
                        )

                    [gma] => Array
                        (
                            [0] => Glyma.15G177300
                            [1] => Glyma.20G037200
                            [2] => Glyma.19G068000
                            [3] => Glyma.20G060800
                            [4] => Glyma.15G210800
                            [5] => Glyma.18G122400
                            [6] => Glyma.18G150700
                            [7] => Glyma.03G079900
                            [8] => Glyma.14G146500
                            [9] => Glyma.20G059900
                            [10] => Glyma.07G119600
                            [11] => Glyma.14G141100
                            [12] => Glyma.06G232700
                            [13] => Glyma.09G096400
                            [14] => Glyma.19G100300
                            [15] => Glyma.14G146600
                            [16] => Glyma.11G160800
                            [17] => Glyma.05G072900
                            [18] => Glyma.08G289400
                            [19] => Glyma.09G151100
                            [20] => Glyma.01G094300
                            [21] => Glyma.07G173200
                            [22] => Glyma.18G122300
                            [23] => Glyma.06G202700
                            [24] => Glyma.20G030000
                            [25] => Glyma.18G156400
                            [26] => Glyma.01G130900
                        )

                    [lja] => Array
                        (
                            [0] => Lj4g0013407
                            [1] => Lj1g0013168
                            [2] => Lj2g0018729
                            [3] => Lj6g0014333
                            [4] => Lj2g0014614
                            [5] => Lj1g0020144
                            [6] => Lj5g0006538
                            [7] => LjContig00408g0026416
                            [8] => LjContig00562g0026224
                            [9] => Lj4g0023820
                            [10] => Lj1g0013324
                            [11] => Lj1g0019916
                            [12] => Lj3g0009331
                            [13] => Lj3g0014470
                            [14] => Lj1g0004876
                            [15] => Lj3g0017745
                            [16] => Lj6g0009158
                            [17] => LjContig00080g0019961
                            [18] => Lj3g0020463
                            [19] => LjContig00506g0000245
                            [20] => Lj5g0012305
                            [21] => Lj3g0021112
                            [22] => Lj3g0024906
                            [23] => Lj6g0015358
                            [24] => Lj2g0025940
                            [25] => Lj2g0009501
                            [26] => Lj1g0002293
                            [27] => Lj1g0015392
                            [28] => Lj2g0002189
                            [29] => Lj3g0001164
                            [30] => Lj5g0017108
                            [31] => Lj2g0019716
                            [32] => Lj4g0018844
                            [33] => Lj2g0012339
                            [34] => Lj1g0000788
                            [35] => LjContig00155g0016901
                            [36] => Lj5g0027822
                            [37] => Lj1g0026464
                            [38] => LjContig00272g0003804
                            [39] => Lj1g0016672
                            [40] => Lj2g0004387
                            [41] => Lj4g0023280
                            [42] => Lj2g0028079
                            [43] => Lj1g0005560
                            [44] => Lj2g0010792
                            [45] => Lj2g0026449
                            [46] => Lj3g0011191
                            [47] => Lj4g0027308
                            [48] => Lj6g0006038
                            [49] => Lj2g0026023
                        )

                    [tpr] => Array
                        (
                            [0] => TPR.G22094
                            [1] => TPR.G9238
                            [2] => TPR.G39902
                            [3] => TPR.G16515
                            [4] => TPR.G30711
                            [5] => TPR.G39624
                            [6] => TPR.G10845
                            [7] => TPR.G40709
                            [8] => TPR.G35396
                            [9] => TPR.G3937
                            [10] => TPR.G40697
                        )

                    [gra] => Array
                        (
                            [0] => Gorai.003G148400
                            [1] => Gorai.003G159900
                            [2] => Gorai.005G169400
                            [3] => Gorai.013G120300
                            [4] => Gorai.008G129700
                            [5] => Gorai.001G201500
                            [6] => Gorai.005G226600
                            [7] => Gorai.007G262100
                            [8] => Gorai.013G103100
                            [9] => Gorai.009G307900
                            [10] => Gorai.012G096500
                            [11] => Gorai.007G206600
                            [12] => Gorai.003G115300
                            [13] => Gorai.013G130000
                            [14] => Gorai.001G087300
                            [15] => Gorai.010G157800
                            [16] => Gorai.008G169100
                            [17] => Gorai.001G115800
                            [18] => Gorai.002G201500
                            [19] => Gorai.003G084600
                            [20] => Gorai.010G130200
                            [21] => Gorai.004G224200
                            [22] => Gorai.006G001200
                            [23] => Gorai.001G169900
                            [24] => Gorai.011G163800
                            [25] => Gorai.005G125200
                        )

                    [ama] => Array
                        (
                            [0] => MSTRG.8973
                            [1] => MSTRG.23897
                        )

                    [esa] => Array
                        (
                            [0] => Thhalv10024098m.g
                            [1] => Thhalv10012334m.g
                            [2] => Thhalv10024111m.g
                            [3] => Thhalv10002268m.g
                            [4] => Thhalv10002329m.g
                            [5] => Thhalv10001275m.g
                            [6] => Thhalv10009827m.g
                            [7] => Thhalv10023048m.g
                            [8] => Thhalv10023798m.g
                            [9] => Thhalv10022480m.g
                        )

                    [oeu] => Array
                        (
                            [0] => Oeu015188.1
                            [1] => Oeu022516.1
                            [2] => Oeu007102.1
                            [3] => Oeu008148.1
                            [4] => Oeu064343.1
                            [5] => Oeu064527.1
                            [6] => Oeu048057.1
                            [7] => Oeu045360.1
                            [8] => Oeu050619.1
                            [9] => Oeu064487.1
                        )

                    [car] => Array
                        (
                            [0] => Ca_22769_v3
                            [1] => Ca_07003_v3
                            [2] => Ca_26786_v3
                            [3] => Ca_18984_v3
                            [4] => Ca_04070_v3
                            [5] => Ca_23932_v3
                            [6] => Ca_03828_v3
                            [7] => Ca_19597_v3
                            [8] => Ca_03988_v3
                        )

                    [cil] => Array
                        (
                            [0] => CiPaw.04G053800
                            [1] => CiPaw.08G029600
                            [2] => CiPaw.03G092700
                            [3] => CiPaw.01G104600
                            [4] => CiPaw.03G066400
                            [5] => CiPaw.02G081200
                        )

                    [egut] => Array
                        (
                            [0] => Migut.O00086
                            [1] => Migut.O00085
                            [2] => Migut.O00084
                            [3] => Migut.O00081
                            [4] => Migut.H01165
                        )

                    [bna] => Array
                        (
                            [0] => C05p32790
                        )

                    [han] => Array
                        (
                            [0] => HanXRQChr02g0042331
                            [1] => HanXRQChr11g0333631
                        )

                    [sly] => Array
                        (
                            [0] => Solyc07g025280.1
                        )

                    [cme] => Array
                        (
                            [0] => MELO3C026718.2
                            [1] => MELO3C004850.2
                            [2] => MELO3C013380.2
                            [3] => MELO3C028612.2
                            [4] => MELO3C008564.2
                            [5] => MELO3C022767.2
                            [6] => MELO3C032329.2
                            [7] => MELO3C003851.2
                            [8] => MELO3C002890.2
                            [9] => MELO3C031980.2
                            [10] => MELO3C030587.2
                            [11] => MELO3C027490.2
                            [12] => MELO3C030509.2
                            [13] => MELO3C026406.2
                        )

                    [can] => Array
                        (
                            [0] => CAN.G362.35
                            [1] => CAN.G150.7
                        )

                    [sun] => Array
                        (
                            [0] => Hund20235
                            [1] => Hund08072
                            [2] => Hund12297
                            [3] => Hund10648
                            [4] => Hund10602
                            [5] => Hund20332
                            [6] => Hund15556
                        )

                    [mes] => Array
                        (
                            [0] => Manes.17G002683
                            [1] => Manes.17G018812
                            [2] => Manes.06G001751
                            [3] => Manes.05G131901
                            [4] => Manes.16G055925
                            [5] => Manes.09G089621
                            [6] => Manes.16G057426
                            [7] => Manes.13G076999
                            [8] => Manes.S095214
                            [9] => Manes.10G080301
                            [10] => Manes.07G055364
                            [11] => Manes.07G055686
                            [12] => Manes.11G096250
                            [13] => Manes.10G055732
                            [14] => Manes.07G056008
                            [15] => Manes.04G156550
                            [16] => Manes.10G066150
                        )

                    [cla] => Array
                        (
                            [0] => ClCG03G013730
                            [1] => ClCG10G003450
                        )

                    [spe] => Array
                        (
                            [0] => Sopen12g001100
                            [1] => Sopen01g014030
                            [2] => Sopen02g001730
                            [3] => Sopen10g010850
                            [4] => Sopen11g016230
                            [5] => Sopen09g014910
                            [6] => Sopen04g017720
                            [7] => Sopen07g010610
                            [8] => Sopen09g015640
                            [9] => Sopen12g012220
                            [10] => Sopen01g009070
                            [11] => Sopen09g015100
                            [12] => Sopen11g007840
                            [13] => Sopen10g016530
                            [14] => Sopen01g025440
                            [15] => Sopen09g015140
                            [16] => Sopen05g019960
                            [17] => Sopen09g015650
                            [18] => Sopen05g024500
                            [19] => Sopen11g016660
                            [20] => Sopen12g012480
                            [21] => Sopen03g014160
                            [22] => Sopen11g007830
                        )

                    [hma] => Array
                        (
                            [0] => Hma1.2p1_0106F.1_g050930
                            [1] => Hma1.2p1_0213F.1_g090600
                        )

                    [amhyb] => Array
                        (
                            [0] => Ah.04g160570
                        )

                    [nta] => Array
                        (
                            [0] => Nitab4.5_0003660g0020
                            [1] => Nitab4.5_0003927g0030
                            [2] => Nitab4.5_0000218g0020
                            [3] => Nitab4.5_0001302g0040
                            [4] => Nitab4.5_0003085g0030
                            [5] => Nitab4.5_0000274g0170
                            [6] => Nitab4.5_0003796g0110
                            [7] => Nitab4.5_0008503g0020
                            [8] => Nitab4.5_0000125g0390
                        )

                    [mbi] => Array
                        (
                            [0] => MBI17_g11095_MAGBIO
                        )

                    [qlo] => Array
                        (
                            [0] => QL07p026138
                        )

                    [acertr] => Array
                        (
                            [0] => Atru.chr1.2247
                            [1] => Atru.chr4.268
                            [2] => Atru.chr1.207
                        )

                    [sed] => Array
                        (
                            [0] => Sed0023676
                        )

                    [stu] => Array
                        (
                            [0] => PGSC0003DMG400036915
                        )

                )

            [gene_id] => PGSC0003DMG400036915
            [gf_types_information] => Array
                (
                    [HOMFAM] => Array
                        (
                            [id] => HOMFAM
                            [name] => Homologous gene family
                            [gene_type] => coding
                            [parent_id] => 
                            [ancestry] => homology
                        )

                    [ORTHOFAM] => Array
                        (
                            [id] => ORTHOFAM
                            [name] => Orthologous gene family
                            [gene_type] => coding
                            [parent_id] => HOMFAM
                            [ancestry] => orthology
                        )

                )

            [gf_types_configuration] => Array
                (
                    [HOMFAM] => Array
                        (
                            [order] => 1
                            [show_parentless_subfamilies] => false
                            [show_table] => true
                            [show_orphan] => 
                        )

                    [ORTHOFAM] => Array
                        (
                            [order] => 2
                            [show_parentless_subfamilies] => false
                            [show_table] => true
                            [show_orphan] => 
                        )

                )

            [all_species] => Array
                (
                    [acertr] => Array
                        (
                            [species] => acertr
                            [common_name] => Acer truncatum
                            [tax_id] => 47965
                            [version] => v2.0
                        )

                    [ach] => Array
                        (
                            [species] => ach
                            [common_name] => Actinidia chinensis
                            [tax_id] => 3625
                            [version] => V3.0
                        )

                    [aar] => Array
                        (
                            [species] => aar
                            [common_name] => Aethionema arabicum
                            [tax_id] => 228871
                            [version] => v3.1
                        )

                    [amhyb] => Array
                        (
                            [species] => amhyb
                            [common_name] => Amaranthus hybridus
                            [tax_id] => 3565
                            [version] => v1.0
                        )

                    [atr] => Array
                        (
                            [species] => atr
                            [common_name] => Amborella trichopoda
                            [tax_id] => 13333
                            [version] => JGI v1.0
                        )

                    [aag] => Array
                        (
                            [species] => aag
                            [common_name] => Anthoceros agrestis
                            [tax_id] => 41834
                            [version] => v1.1
                        )

                    [aox] => Array
                        (
                            [species] => aox
                            [common_name] => Aquilegia oxysepala
                            [tax_id] => 432649
                            [version] => v1.0
                        )

                    [aly] => Array
                        (
                            [species] => aly
                            [common_name] => Arabidopsis lyrata
                            [tax_id] => 59689
                            [version] => JGI v2.1
                        )

                    [ath] => Array
                        (
                            [species] => ath
                            [common_name] => Arabidopsis thaliana
                            [tax_id] => 3702
                            [version] => Araport11
                        )

                    [arhy] => Array
                        (
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [tax_id] => 3818
                            [version] => v1.0
                        )

                    [ama] => Array
                        (
                            [species] => ama
                            [common_name] => Avicennia marina
                            [tax_id] => 82927
                            [version] => v1.1 20200527
                        )

                    [bvu] => Array
                        (
                            [species] => bvu
                            [common_name] => Beta vulgaris
                            [tax_id] => 161934
                            [version] => EL10_1.0
                        )

                    [bca] => Array
                        (
                            [species] => bca
                            [common_name] => Brassica carinata
                            [tax_id] => 52824
                            [version] => V1.0
                        )

                    [bna] => Array
                        (
                            [species] => bna
                            [common_name] => Brassica napus
                            [tax_id] => 3708
                            [version] => v2.0
                        )

                    [bol] => Array
                        (
                            [species] => bol
                            [common_name] => Brassica oleracea
                            [tax_id] => 109376
                            [version] => v1.0
                        )

                    [bra] => Array
                        (
                            [species] => bra
                            [common_name] => Brassica rapa
                            [tax_id] => 3711
                            [version] => v1.0
                        )

                    [camsi] => Array
                        (
                            [species] => camsi
                            [common_name] => Camellia sinensis var. sinensis
                            [tax_id] => 542762
                            [version] => CSS_ChrLev_20200506
                        )

                    [cansat] => Array
                        (
                            [species] => cansat
                            [common_name] => Cannabis sativa
                            [tax_id] => 3483
                            [version] => cs10
                        )

                    [cru] => Array
                        (
                            [species] => cru
                            [common_name] => Capsella rubella
                            [tax_id] => 81985
                            [version] => JGI v1.1
                        )

                    [can] => Array
                        (
                            [species] => can
                            [common_name] => Capsicum annuum
                            [tax_id] => 4072
                            [version] => Pepper Genome v2.0
                        )

                    [chi] => Array
                        (
                            [species] => chi
                            [common_name] => Cardamine hirsuta
                            [tax_id] => 50463
                            [version] => v1.0
                        )

                    [cpa] => Array
                        (
                            [species] => cpa
                            [common_name] => Carica papaya
                            [tax_id] => 3649
                            [version] => JGI ASGPB0.4
                        )

                    [cfa] => Array
                        (
                            [species] => cfa
                            [common_name] => Carpinus fangiana
                            [tax_id] => 176857
                            [version] => v1.0
                        )

                    [cil] => Array
                        (
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [tax_id] => 32201
                            [version] => v1.1
                        )

                    [cde] => Array
                        (
                            [species] => cde
                            [common_name] => Ceratophyllum demersum
                            [tax_id] => 4428
                            [version] => v1.0
                        )

                    [cbr] => Array
                        (
                            [species] => cbr
                            [common_name] => Chara braunii
                            [tax_id] => 69332
                            [version] => Cbr1.0
                        )

                    [cqu] => Array
                        (
                            [species] => cqu
                            [common_name] => Chenopodium quinoa
                            [tax_id] => 63459
                            [version] => KAUST v1.0
                        )

                    [cre] => Array
                        (
                            [species] => cre
                            [common_name] => Chlamydomonas reinhardtii
                            [tax_id] => 3055
                            [version] => JGI v5.5
                        )

                    [car] => Array
                        (
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [tax_id] => 3827
                            [version] => v3.0
                        )

                    [cla] => Array
                        (
                            [species] => cla
                            [common_name] => Citrullus lanatus
                            [tax_id] => 3654
                            [version] => WCG v2.0
                        )

                    [ccl] => Array
                        (
                            [species] => ccl
                            [common_name] => Citrus clementina
                            [tax_id] => 85681
                            [version] => JGI v1.0
                        )

                    [ccan] => Array
                        (
                            [species] => ccan
                            [common_name] => Coffea canephora
                            [tax_id] => 49390
                            [version] => Coffee Genome Hub v1
                        )

                    [col] => Array
                        (
                            [species] => col
                            [common_name] => Corchorus olitorius
                            [tax_id] => 93759
                            [version] => GenBank v1.0
                        )

                    [cav] => Array
                        (
                            [species] => cav
                            [common_name] => Corylus avellana
                            [tax_id] => 13451
                            [version] => v1.0
                        )

                    [cme] => Array
                        (
                            [species] => cme
                            [common_name] => Cucumis melo
                            [tax_id] => 3656
                            [version] => Melonomics v3.6.1
                        )

                    [csa] => Array
                        (
                            [species] => csa
                            [common_name] => Cucumis sativus L.
                            [tax_id] => 3659
                            [version] => v3.0
                        )

                    [dca] => Array
                        (
                            [species] => dca
                            [common_name] => Daucus carota
                            [tax_id] => 4039
                            [version] => JGI v2.0
                        )

                    [din] => Array
                        (
                            [species] => din
                            [common_name] => Davidia involucrata
                            [tax_id] => 16924
                            [version] => v1.0
                        )

                    [dzi] => Array
                        (
                            [species] => dzi
                            [common_name] => Durio zibethinus
                            [tax_id] => 66656
                            [version] => Duzib1.0
                        )

                    [eca] => Array
                        (
                            [species] => eca
                            [common_name] => Erigeron canadensis
                            [tax_id] => 72917
                            [version] => V1.0
                        )

                    [egut] => Array
                        (
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [tax_id] => 4155
                            [version] => v2.0
                        )

                    [egr] => Array
                        (
                            [species] => egr
                            [common_name] => Eucalyptus grandis
                            [tax_id] => 71139
                            [version] => v2.0
                        )

                    [esa] => Array
                        (
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [tax_id] => 72664
                            [version] => v1.0
                        )

                    [fve] => Array
                        (
                            [species] => fve
                            [common_name] => Fragaria vesca
                            [tax_id] => 57918
                            [version] => V4.0.a2
                        )

                    [fan] => Array
                        (
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [tax_id] => 3747
                            [version] => V1.0.a1
                        )

                    [gma] => Array
                        (
                            [species] => gma
                            [common_name] => Glycine max
                            [tax_id] => 3847
                            [version] => JGI Wm82.a4.v1
                        )

                    [ghi] => Array
                        (
                            [species] => ghi
                            [common_name] => Gossypium hirsutum
                            [tax_id] => 3635
                            [version] => v2.1
                        )

                    [gra] => Array
                        (
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [tax_id] => 29730
                            [version] => v2.1
                        )

                    [han] => Array
                        (
                            [species] => han
                            [common_name] => Helianthus annuus
                            [tax_id] => 4232
                            [version] => r1.2
                        )

                    [hma] => Array
                        (
                            [species] => hma
                            [common_name] => Hydrangea macrophylla
                            [tax_id] => 23110
                            [version] => v2.1
                        )

                    [lsa] => Array
                        (
                            [species] => lsa
                            [common_name] => Lactuca sativa
                            [tax_id] => 4236
                            [version] => v8.0
                        )

                    [lonja] => Array
                        (
                            [species] => lonja
                            [common_name] => Lonicera japonica
                            [tax_id] => 105884
                            [version] => v1.0
                        )

                    [lja] => Array
                        (
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [tax_id] => 34305
                            [version] => Lj1.0v1
                        )

                    [lal] => Array
                        (
                            [species] => lal
                            [common_name] => Lupinus albus
                            [tax_id] => 3870
                            [version] => v1.0
                        )

                    [mbi] => Array
                        (
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [tax_id] => 86725
                            [version] => v1.0
                        )

                    [mdo] => Array
                        (
                            [species] => mdo
                            [common_name] => Malus domestica
                            [tax_id] => 3750
                            [version] => GDDH13 v1.1
                        )

                    [mes] => Array
                        (
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [tax_id] => 3983
                            [version] => v8.1
                        )

                    [mpo] => Array
                        (
                            [species] => mpo
                            [common_name] => Marchantia polymorpha
                            [tax_id] => 3197
                            [version] => JGI v3.1
                        )

                    [mtr] => Array
                        (
                            [species] => mtr
                            [common_name] => Medicago truncatula
                            [tax_id] => 3880
                            [version] => JGI Mt4.0v1
                        )

                    [mco] => Array
                        (
                            [species] => mco
                            [common_name] => Micromonas commoda
                            [tax_id] => 296587
                            [version] => JGI v3.0
                        )

                    [nnu] => Array
                        (
                            [species] => nnu
                            [common_name] => Nelumbo nucifera
                            [tax_id] => 4432
                            [version] => v2.0
                        )

                    [nta] => Array
                        (
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [tax_id] => 4097
                            [version] => Edwards2017
                        )

                    [oeu] => Array
                        (
                            [species] => oeu
                            [common_name] => Olea europaea
                            [tax_id] => 4146
                            [version] => v1.0
                        )

                    [osa] => Array
                        (
                            [species] => osa
                            [common_name] => Oryza sativa ssp. japonica
                            [tax_id] => 39947
                            [version] => IRGSP-1.0-2021-05-10
                        )

                    [pso] => Array
                        (
                            [species] => pso
                            [common_name] => Papaver somniferum
                            [tax_id] => 3469
                            [version] => ASM357369v1
                        )

                    [pax] => Array
                        (
                            [species] => pax
                            [common_name] => Petunia axillaris
                            [tax_id] => 33119
                            [version] => Sol Genomics v1.6.2
                        )

                    [pvu] => Array
                        (
                            [species] => pvu
                            [common_name] => Phaseolus vulgaris
                            [tax_id] => 3885
                            [version] => v2.1
                        )

                    [ppa] => Array
                        (
                            [species] => ppa
                            [common_name] => Physcomitrium patens
                            [tax_id] => 3218
                            [version] => JGI v3.3
                        )

                    [psa] => Array
                        (
                            [species] => psa
                            [common_name] => Pisum sativum
                            [tax_id] => 3888
                            [version] => V1.0a
                        )

                    [ptr] => Array
                        (
                            [species] => ptr
                            [common_name] => Populus trichocarpa
                            [tax_id] => 3694
                            [version] => JGI v4.1
                        )

                    [pco] => Array
                        (
                            [species] => pco
                            [common_name] => Prasinoderma coloniale
                            [tax_id] => 156133
                            [version] => v1.0
                        )

                    [ppe] => Array
                        (
                            [species] => ppe
                            [common_name] => Prunus persica
                            [tax_id] => 3760
                            [version] => v2.1
                        )

                    [pgr] => Array
                        (
                            [species] => pgr
                            [common_name] => Punica granatum
                            [tax_id] => 22663
                            [version] => ASM765513v2
                        )

                    [qlo] => Array
                        (
                            [species] => qlo
                            [common_name] => Quercus lobata
                            [tax_id] => 97700
                            [version] => v3.0
                        )

                    [rsi] => Array
                        (
                            [species] => rsi
                            [common_name] => Rhododendron simsii
                            [tax_id] => 118357
                            [version] => v1.0
                        )

                    [rch] => Array
                        (
                            [species] => rch
                            [common_name] => Rosa chinensis
                            [tax_id] => 74649
                            [version] => v2.0
                        )

                    [sbr] => Array
                        (
                            [species] => sbr
                            [common_name] => Salix brachista
                            [tax_id] => 2182728
                            [version] => v1.0
                        )

                    [sbo] => Array
                        (
                            [species] => sbo
                            [common_name] => Salvia bowleyana
                            [tax_id] => 424416
                            [version] => v1.0
                        )

                    [shi] => Array
                        (
                            [species] => shi
                            [common_name] => Sapria himalayana
                            [tax_id] => 289637
                            [version] => v1.0
                        )

                    [spa] => Array
                        (
                            [species] => spa
                            [common_name] => Schrenkiella parvula
                            [tax_id] => 98039
                            [version] => v2.2
                        )

                    [sed] => Array
                        (
                            [species] => sed
                            [common_name] => Sechium edule
                            [tax_id] => 184140
                            [version] => v1.0
                        )

                    [smo] => Array
                        (
                            [species] => smo
                            [common_name] => Selaginella moellendorffii
                            [tax_id] => 88036
                            [version] => v1.0
                        )

                    [sun] => Array
                        (
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [tax_id] => 176265
                            [version] => v1.0
                        )

                    [sgi] => Array
                        (
                            [species] => sgi
                            [common_name] => Sequoiadendron giganteum
                            [tax_id] => 99814
                            [version] => V2.0
                        )

                    [sci] => Array
                        (
                            [species] => sci
                            [common_name] => Simmondsia chinensis
                            [tax_id] => 3999
                            [version] => sc1
                        )

                    [sly] => Array
                        (
                            [species] => sly
                            [common_name] => Solanum lycopersicum
                            [tax_id] => 4081
                            [version] => ITAG4.0
                        )

                    [spe] => Array
                        (
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [tax_id] => 28526
                            [version] => V2.0
                        )

                    [stu] => Array
                        (
                            [species] => stu
                            [common_name] => Solanum tuberosum
                            [tax_id] => 4113
                            [version] => JGI v4.03
                        )

                    [sas] => Array
                        (
                            [species] => sas
                            [common_name] => Striga asiatica
                            [tax_id] => 4170
                            [version] => v2.02
                        )

                    [tha] => Array
                        (
                            [species] => tha
                            [common_name] => Tarenaya hassleriana
                            [tax_id] => 28532
                            [version] => RefSeq v1
                        )

                    [tca] => Array
                        (
                            [species] => tca
                            [common_name] => Theobroma cacao
                            [tax_id] => 3641
                            [version] => V2.1
                        )

                    [tpr] => Array
                        (
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [tax_id] => 57577
                            [version] => V2.0
                        )

                    [twi] => Array
                        (
                            [species] => twi
                            [common_name] => Tripterygium wilfordii
                            [tax_id] => 458696
                            [version] => ASM1340144v1
                        )

                    [tar] => Array
                        (
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [tax_id] => 4407
                            [version] => v1.0
                        )

                    [ugi] => Array
                        (
                            [species] => ugi
                            [common_name] => Utricularia gibba
                            [tax_id] => 13748
                            [version] => v1.1F
                        )

                    [vma] => Array
                        (
                            [species] => vma
                            [common_name] => Vaccinium macrocarpon
                            [tax_id] => 13750
                            [version] => V1.0
                        )

                    [vpl] => Array
                        (
                            [species] => vpl
                            [common_name] => Vanilla planifolia
                            [tax_id] => 51239
                            [version] => Elo Vpla-A Principal v1.0
                        )

                    [vmu] => Array
                        (
                            [species] => vmu
                            [common_name] => Vigna mungo
                            [tax_id] => 3915
                            [version] => ASM1342719v1
                        )

                    [vvi] => Array
                        (
                            [species] => vvi
                            [common_name] => Vitis vinifera
                            [tax_id] => 29760
                            [version] => Genoscope.12x
                        )

                    [zma] => Array
                        (
                            [species] => zma
                            [common_name] => Zea mays
                            [tax_id] => 4577
                            [version] => NAM v5.0
                        )

                )

            [allow_async_use] => 1
            [sidebar_information] => Array
                (
                    [type] => gene_id
                    [id] => arahy.Tifrunner.gnm1.ann1.87PAU8
                )

            [data_identifier] => arahy.Tifrunner.gnm1.ann1.87PAU8
            [data_type] => gene_id
        )

    [view] => custom_tree_creation
    [layout] => toolbox_layout
    [autoRender] => 1
    [autoLayout] => 1
    [Components] => ComponentCollection Object
        (
            [_Controller:protected] => AnalysisController Object
 *RECURSION*
            [_enabled:protected] => Array
                (
                    [Session] => Array
                        (
                            [0] => 10
                            [1] => 1
                        )

                    [DataUtils] => Array
                        (
                            [0] => 10
                            [1] => 2
                        )

                    [FunctionalAnnotationUtils] => Array
                        (
                            [0] => 10
                            [1] => 3
                        )

                    [GeneFamilies] => Array
                        (
                            [0] => 10
                            [1] => 4
                        )

                    [Organism] => Array
                        (
                            [0] => 10
                            [1] => 5
                        )

                    [Blast] => Array
                        (
                            [0] => 10
                            [1] => 6
                        )

                    [WorkbenchUtils] => Array
                        (
                            [0] => 10
                            [1] => 7
                        )

                    [PhylogeneticModuleUtils] => Array
                        (
                            [0] => 10
                            [1] => 8
                        )

                    [ExternalPrograms] => Array
                        (
                            [0] => 10
                            [1] => 9
                        )

                    [FastaUtils] => Array
                        (
                            [0] => 10
                            [1] => 10
                        )

                    [MsaUtils] => Array
                        (
                            [0] => 10
                            [1] => 11
                        )

                    [PhylogeneticUtils] => Array
                        (
                            [0] => 10
                            [1] => 12
                        )

                    [Sequence] => Array
                        (
                            [0] => 10
                            [1] => 13
                        )

                    [RequestHandler] => Array
                        (
                            [0] => 10
                            [1] => 14
                        )

                )

            [_loaded:protected] => Array
                (
                    [Session] => SessionComponent Object
                        (
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [DataUtils] => DataUtilsComponent Object
                        (
                            [name] => DataUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                    [1] => FunctionalUtils
                                    [2] => GeneFamilies
                                    [3] => GenomeBrowser
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FunctionalUtils] => Array
                                        (
                                            [class] => FunctionalUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [GeneFamilies] => Array
                                        (
                                            [class] => GeneFamilies
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [GenomeBrowser] => Array
                                        (
                                            [class] => GenomeBrowser
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                        )

                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                        (
                            [name] => FunctionalAnnotationUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => FunctionalUtils
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [FunctionalUtils] => Array
                                        (
                                            [class] => FunctionalUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [GeneFamilies] => GeneFamiliesComponent Object
                        (
                            [name] => GeneFamilies
                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [Organism] => OrganismComponent Object
                        (
                            [name] => Organism
                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => GenomeBrowser
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [GenomeBrowser] => Array
                                        (
                                            [class] => GenomeBrowser
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [Blast] => BlastComponent Object
                        (
                            [name] => Blast
                            [controller] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                        (
                            [name] => WorkbenchUtils
                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                    [1] => FormUtils
                                    [2] => FunctionalUtils
                                    [3] => GeneFamilies
                                    [4] => WorkbenchSharedAccessRights
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FormUtils] => Array
                                        (
                                            [class] => FormUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FunctionalUtils] => Array
                                        (
                                            [class] => FunctionalUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [GeneFamilies] => Array
                                        (
                                            [class] => GeneFamilies
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [WorkbenchSharedAccessRights] => Array
                                        (
                                            [class] => WorkbenchSharedAccessRights
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                        (
                            [name] => PhylogeneticModuleUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                    [1] => FastaUtils
                                    [2] => MsaUtils
                                    [3] => PhylogeneticUtils
                                    [4] => Sequence
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FastaUtils] => Array
                                        (
                                            [class] => FastaUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [MsaUtils] => Array
                                        (
                                            [class] => MsaUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [PhylogeneticUtils] => Array
                                        (
                                            [class] => PhylogeneticUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [Sequence] => Array
                                        (
                                            [class] => Sequence
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [ExternalPrograms] => ExternalProgramsComponent Object
                        (
                            [name] => ExternalPrograms
                            [components] => Array
                                (
                                    [0] => FastaUtils
                                )

                            [program_paths:ExternalProgramsComponent:private] => Array
                                (
                                    [java] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => java/x86_64/21.0.2
                                                        )

                                                    [command] => java -Djava.awt.headless=true
                                                )

                                            [local_settings] => java -Djava.awt.headless=true
                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                        )

                                    [perl] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => perl
                                                        )

                                                    [command] => perl -w
                                                )

                                            [local_settings] => /usr/bin/perl
                                        )

                                    [bash] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                        )

                                                    [command] => 
                                                )

                                            [local_settings] => 
                                        )

                                    [bedops] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => bedops/x86_64/2.4.37
                                                        )

                                                    [command] => 
                                                )

                                            [local_settings] => 
                                        )

                                    [blastdbcmd] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => blast
                                                        )

                                                    [command] => blastdbcmd
                                                )

                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                        )

                                    [blast] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => blast
                                                        )

                                                    [command] => 
                                                )

                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                        )

                                    [muscle] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => muscle/x86_64/3.8.31
                                                        )

                                                )

                                        )

                                    [mafft] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => mafft/x86_64/7.187
                                                        )

                                                )

                                        )

                                    [phyml] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => phyml/x86_64/20150219
                                                        )

                                                )

                                        )

                                    [fasttree] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => fasttree/x86_64/2.1.7
                                                        )

                                                )

                                        )

                                    [raxml] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => raxml/x86_64/8.2.8
                                                        )

                                                )

                                        )

                                    [iqtree] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => iqtree/x86_64/1.5.5
                                                        )

                                                )

                                        )

                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [FastaUtils] => Array
                                        (
                                            [class] => FastaUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [FastaUtils] => FastaUtilsComponent Object
                        (
                            [name] => FastaUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [MsaUtils] => MsaUtilsComponent Object
                        (
                            [name] => MsaUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                        (
                            [name] => PhylogeneticUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [Sequence] => SequenceComponent Object
                        (
                            [name] => Sequence
                            [components] => Array
                                (
                                    [0] => Blast
                                    [1] => Coordinates
                                    [2] => ExternalPrograms
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [Blast] => Array
                                        (
                                            [class] => Blast
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [Coordinates] => Array
                                        (
                                            [class] => Coordinates
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                            [controller] => AnalysisController Object
 *RECURSION*
                        )

                    [RequestHandler] => RequestHandlerComponent Object
                        (
                            [ajaxLayout] => ajax
                            [enabled] => 1
                            [request] => CakeRequest Object
                                (
                                    [params] => Array
                                        (
                                            [plugin] => 
                                            [controller] => analysis
                                            [action] => custom_tree_creation
                                            [named] => Array
                                                (
                                                )

                                            [pass] => Array
                                                (
                                                    [0] => gene_id
                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                )

                                            [isAjax] => 
                                        )

                                    [data] => Array
                                        (
                                        )

                                    [query] => Array
                                        (
                                        )

                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                    [base] => /plaza.dev/_dev_instances/feedback
                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                    [_detectors:protected] => Array
                                        (
                                            [get] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => GET
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                                            [patch] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PATCH
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                                            [post] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => POST
                                                )

                                            [put] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PUT
                                                )

                                            [delete] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => DELETE
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                                            [head] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => HEAD
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                                            [options] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => OPTIONS
                                                )

                                            [ssl] => Array
                                                (
                                                    [env] => HTTPS
                                                    [value] => 1
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                                            [ajax] => Array
                                                (
                                                    [env] => HTTP_X_REQUESTED_WITH
                                                    [value] => XMLHttpRequest
                                                )

                                            [flash] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [pattern] => /^(Shockwave|Adobe) Flash/
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                                            [mobile] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [options] => Array
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                                                            [1] => AvantGo
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                                                            [3] => BlackBerry
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                                                            [5] => Fennec
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                                                            [8] => iPad
                                                            [9] => J2ME
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                                                            [13] => Opera Mini
                                                            [14] => Opera Mobi
                                                            [15] => PalmOS
                                                            [16] => PalmSource
                                                            [17] => portalmmm
                                                            [18] => Plucker
                                                            [19] => ReqwirelessWeb
                                                            [20] => SonyEricsson
                                                            [21] => Symbian
                                                            [22] => UP\.Browser
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                                                            [24] => Windows CE
                                                            [25] => Windows Phone OS
                                                            [26] => Xiino
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                                                )

                                            [requested] => Array
                                                (
                                                    [param] => requested
                                                    [value] => 1
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                                            [json] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/json
                                                        )

                                                    [param] => ext
                                                    [value] => json
                                                )

                                            [xml] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
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                                                    [param] => ext
                                                    [value] => xml
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                                        )

                                    [_input:protected] => 
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                            [response] => CakeResponse Object
                                (
                                    [_statusCodes:protected] => Array
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                                            [101] => Switching Protocols
                                            [200] => OK
                                            [201] => Created
                                            [202] => Accepted
                                            [203] => Non-Authoritative Information
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                                            [205] => Reset Content
                                            [206] => Partial Content
                                            [300] => Multiple Choices
                                            [301] => Moved Permanently
                                            [302] => Found
                                            [303] => See Other
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                                            [305] => Use Proxy
                                            [307] => Temporary Redirect
                                            [400] => Bad Request
                                            [401] => Unauthorized
                                            [402] => Payment Required
                                            [403] => Forbidden
                                            [404] => Not Found
                                            [405] => Method Not Allowed
                                            [406] => Not Acceptable
                                            [407] => Proxy Authentication Required
                                            [408] => Request Time-out
                                            [409] => Conflict
                                            [410] => Gone
                                            [411] => Length Required
                                            [412] => Precondition Failed
                                            [413] => Request Entity Too Large
                                            [414] => Request-URI Too Large
                                            [415] => Unsupported Media Type
                                            [416] => Requested range not satisfiable
                                            [417] => Expectation Failed
                                            [429] => Too Many Requests
                                            [500] => Internal Server Error
                                            [501] => Not Implemented
                                            [502] => Bad Gateway
                                            [503] => Service Unavailable
                                            [504] => Gateway Time-out
                                            [505] => Unsupported Version
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                                    [_mimeTypes:protected] => Array
                                        (
                                            [html] => Array
                                                (
                                                    [0] => text/html
                                                    [1] => */*
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                                            [json] => application/json
                                            [xml] => Array
                                                (
                                                    [0] => application/xml
                                                    [1] => text/xml
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                                            [rss] => application/rss+xml
                                            [ai] => application/postscript
                                            [bcpio] => application/x-bcpio
                                            [bin] => application/octet-stream
                                            [ccad] => application/clariscad
                                            [cdf] => application/x-netcdf
                                            [class] => application/octet-stream
                                            [cpio] => application/x-cpio
                                            [cpt] => application/mac-compactpro
                                            [csh] => application/x-csh
                                            [csv] => Array
                                                (
                                                    [0] => text/csv
                                                    [1] => application/vnd.ms-excel
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                                            [dcr] => application/x-director
                                            [dir] => application/x-director
                                            [dms] => application/octet-stream
                                            [doc] => application/msword
                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                            [drw] => application/drafting
                                            [dvi] => application/x-dvi
                                            [dwg] => application/acad
                                            [dxf] => application/dxf
                                            [dxr] => application/x-director
                                            [eot] => application/vnd.ms-fontobject
                                            [eps] => application/postscript
                                            [exe] => application/octet-stream
                                            [ez] => application/andrew-inset
                                            [flv] => video/x-flv
                                            [gtar] => application/x-gtar
                                            [gz] => application/x-gzip
                                            [bz2] => application/x-bzip
                                            [7z] => application/x-7z-compressed
                                            [hdf] => application/x-hdf
                                            [hqx] => application/mac-binhex40
                                            [ico] => image/x-icon
                                            [ips] => application/x-ipscript
                                            [ipx] => application/x-ipix
                                            [js] => application/javascript
                                            [jsonapi] => application/vnd.api+json
                                            [latex] => application/x-latex
                                            [lha] => application/octet-stream
                                            [lsp] => application/x-lisp
                                            [lzh] => application/octet-stream
                                            [man] => application/x-troff-man
                                            [me] => application/x-troff-me
                                            [mif] => application/vnd.mif
                                            [ms] => application/x-troff-ms
                                            [nc] => application/x-netcdf
                                            [oda] => application/oda
                                            [otf] => font/otf
                                            [pdf] => application/pdf
                                            [pgn] => application/x-chess-pgn
                                            [pot] => application/vnd.ms-powerpoint
                                            [pps] => application/vnd.ms-powerpoint
                                            [ppt] => application/vnd.ms-powerpoint
                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                            [ppz] => application/vnd.ms-powerpoint
                                            [pre] => application/x-freelance
                                            [prt] => application/pro_eng
                                            [ps] => application/postscript
                                            [roff] => application/x-troff
                                            [scm] => application/x-lotusscreencam
                                            [set] => application/set
                                            [sh] => application/x-sh
                                            [shar] => application/x-shar
                                            [sit] => application/x-stuffit
                                            [skd] => application/x-koan
                                            [skm] => application/x-koan
                                            [skp] => application/x-koan
                                            [skt] => application/x-koan
                                            [smi] => application/smil
                                            [smil] => application/smil
                                            [sol] => application/solids
                                            [spl] => application/x-futuresplash
                                            [src] => application/x-wais-source
                                            [step] => application/STEP
                                            [stl] => application/SLA
                                            [stp] => application/STEP
                                            [sv4cpio] => application/x-sv4cpio
                                            [sv4crc] => application/x-sv4crc
                                            [svg] => image/svg+xml
                                            [svgz] => image/svg+xml
                                            [swf] => application/x-shockwave-flash
                                            [t] => application/x-troff
                                            [tar] => application/x-tar
                                            [tcl] => application/x-tcl
                                            [tex] => application/x-tex
                                            [texi] => application/x-texinfo
                                            [texinfo] => application/x-texinfo
                                            [tr] => application/x-troff
                                            [tsp] => application/dsptype
                                            [ttc] => font/ttf
                                            [ttf] => font/ttf
                                            [unv] => application/i-deas
                                            [ustar] => application/x-ustar
                                            [vcd] => application/x-cdlink
                                            [vda] => application/vda
                                            [xlc] => application/vnd.ms-excel
                                            [xll] => application/vnd.ms-excel
                                            [xlm] => application/vnd.ms-excel
                                            [xls] => application/vnd.ms-excel
                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                            [xlw] => application/vnd.ms-excel
                                            [zip] => application/zip
                                            [aif] => audio/x-aiff
                                            [aifc] => audio/x-aiff
                                            [aiff] => audio/x-aiff
                                            [au] => audio/basic
                                            [kar] => audio/midi
                                            [mid] => audio/midi
                                            [midi] => audio/midi
                                            [mp2] => audio/mpeg
                                            [mp3] => audio/mpeg
                                            [mpga] => audio/mpeg
                                            [ogg] => audio/ogg
                                            [oga] => audio/ogg
                                            [spx] => audio/ogg
                                            [ra] => audio/x-realaudio
                                            [ram] => audio/x-pn-realaudio
                                            [rm] => audio/x-pn-realaudio
                                            [rpm] => audio/x-pn-realaudio-plugin
                                            [snd] => audio/basic
                                            [tsi] => audio/TSP-audio
                                            [wav] => audio/x-wav
                                            [aac] => audio/aac
                                            [asc] => text/plain
                                            [c] => text/plain
                                            [cc] => text/plain
                                            [css] => text/css
                                            [etx] => text/x-setext
                                            [f] => text/plain
                                            [f90] => text/plain
                                            [h] => text/plain
                                            [hh] => text/plain
                                            [htm] => Array
                                                (
                                                    [0] => text/html
                                                    [1] => */*
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                                            [ics] => text/calendar
                                            [m] => text/plain
                                            [rtf] => text/rtf
                                            [rtx] => text/richtext
                                            [sgm] => text/sgml
                                            [sgml] => text/sgml
                                            [tsv] => text/tab-separated-values
                                            [tpl] => text/template
                                            [txt] => text/plain
                                            [text] => text/plain
                                            [avi] => video/x-msvideo
                                            [fli] => video/x-fli
                                            [mov] => video/quicktime
                                            [movie] => video/x-sgi-movie
                                            [mpe] => video/mpeg
                                            [mpeg] => video/mpeg
                                            [mpg] => video/mpeg
                                            [qt] => video/quicktime
                                            [viv] => video/vnd.vivo
                                            [vivo] => video/vnd.vivo
                                            [ogv] => video/ogg
                                            [webm] => video/webm
                                            [mp4] => video/mp4
                                            [m4v] => video/mp4
                                            [f4v] => video/mp4
                                            [f4p] => video/mp4
                                            [m4a] => audio/mp4
                                            [f4a] => audio/mp4
                                            [f4b] => audio/mp4
                                            [gif] => image/gif
                                            [ief] => image/ief
                                            [jpg] => image/jpeg
                                            [jpeg] => image/jpeg
                                            [jpe] => image/jpeg
                                            [pbm] => image/x-portable-bitmap
                                            [pgm] => image/x-portable-graymap
                                            [png] => image/png
                                            [pnm] => image/x-portable-anymap
                                            [ppm] => image/x-portable-pixmap
                                            [ras] => image/cmu-raster
                                            [rgb] => image/x-rgb
                                            [tif] => image/tiff
                                            [tiff] => image/tiff
                                            [xbm] => image/x-xbitmap
                                            [xpm] => image/x-xpixmap
                                            [xwd] => image/x-xwindowdump
                                            [psd] => Array
                                                (
                                                    [0] => application/photoshop
                                                    [1] => application/psd
                                                    [2] => image/psd
                                                    [3] => image/x-photoshop
                                                    [4] => image/photoshop
                                                    [5] => zz-application/zz-winassoc-psd
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                                            [ice] => x-conference/x-cooltalk
                                            [iges] => model/iges
                                            [igs] => model/iges
                                            [mesh] => model/mesh
                                            [msh] => model/mesh
                                            [silo] => model/mesh
                                            [vrml] => model/vrml
                                            [wrl] => model/vrml
                                            [mime] => www/mime
                                            [pdb] => chemical/x-pdb
                                            [xyz] => chemical/x-pdb
                                            [javascript] => application/javascript
                                            [form] => application/x-www-form-urlencoded
                                            [file] => multipart/form-data
                                            [xhtml] => Array
                                                (
                                                    [0] => application/xhtml+xml
                                                    [1] => application/xhtml
                                                    [2] => text/xhtml
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                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                            [atom] => application/atom+xml
                                            [amf] => application/x-amf
                                            [wap] => Array
                                                (
                                                    [0] => text/vnd.wap.wml
                                                    [1] => text/vnd.wap.wmlscript
                                                    [2] => image/vnd.wap.wbmp
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                                            [wml] => text/vnd.wap.wml
                                            [wmlscript] => text/vnd.wap.wmlscript
                                            [wbmp] => image/vnd.wap.wbmp
                                            [woff] => application/x-font-woff
                                            [webp] => image/webp
                                            [appcache] => text/cache-manifest
                                            [manifest] => text/cache-manifest
                                            [htc] => text/x-component
                                            [rdf] => application/xml
                                            [crx] => application/x-chrome-extension
                                            [oex] => application/x-opera-extension
                                            [xpi] => application/x-xpinstall
                                            [safariextz] => application/octet-stream
                                            [webapp] => application/x-web-app-manifest+json
                                            [vcf] => text/x-vcard
                                            [vtt] => text/vtt
                                            [mkv] => video/x-matroska
                                            [pkpass] => application/vnd.apple.pkpass
                                            [ajax] => text/html
                                        )

                                    [_protocol:protected] => HTTP/1.1
                                    [_status:protected] => 200
                                    [_contentType:protected] => text/html
                                    [_headers:protected] => Array
                                        (
                                        )

                                    [_body:protected] => 
                                    [_file:protected] => 
                                    [_fileRange:protected] => 
                                    [_charset:protected] => UTF-8
                                    [_cacheDirectives:protected] => Array
                                        (
                                        )

                                    [_cookies:protected] => Array
                                        (
                                        )

                                )

                            [ext] => 
                            [_renderType:protected] => 
                            [_inputTypeMap:protected] => Array
                                (
                                    [json] => Array
                                        (
                                            [0] => json_decode
                                            [1] => 1
                                        )

                                    [xml] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                    [1] => convertXml
                                                )

                                        )

                                )

                            [_viewClassMap:protected] => Array
                                (
                                    [json] => Json
                                    [xml] => Xml
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                    [checkHttpCache] => 1
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                            [params] => CakeRequest Object
                                (
                                    [params] => Array
                                        (
                                            [plugin] => 
                                            [controller] => analysis
                                            [action] => custom_tree_creation
                                            [named] => Array
                                                (
                                                )

                                            [pass] => Array
                                                (
                                                    [0] => gene_id
                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                )

                                            [isAjax] => 
                                        )

                                    [data] => Array
                                        (
                                        )

                                    [query] => Array
                                        (
                                        )

                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                    [base] => /plaza.dev/_dev_instances/feedback
                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                    [_detectors:protected] => Array
                                        (
                                            [get] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => GET
                                                )

                                            [patch] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PATCH
                                                )

                                            [post] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => POST
                                                )

                                            [put] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PUT
                                                )

                                            [delete] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => DELETE
                                                )

                                            [head] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => HEAD
                                                )

                                            [options] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => OPTIONS
                                                )

                                            [ssl] => Array
                                                (
                                                    [env] => HTTPS
                                                    [value] => 1
                                                )

                                            [ajax] => Array
                                                (
                                                    [env] => HTTP_X_REQUESTED_WITH
                                                    [value] => XMLHttpRequest
                                                )

                                            [flash] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                )

                                            [mobile] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [options] => Array
                                                        (
                                                            [0] => Android
                                                            [1] => AvantGo
                                                            [2] => BB10
                                                            [3] => BlackBerry
                                                            [4] => DoCoMo
                                                            [5] => Fennec
                                                            [6] => iPod
                                                            [7] => iPhone
                                                            [8] => iPad
                                                            [9] => J2ME
                                                            [10] => MIDP
                                                            [11] => NetFront
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                                                            [13] => Opera Mini
                                                            [14] => Opera Mobi
                                                            [15] => PalmOS
                                                            [16] => PalmSource
                                                            [17] => portalmmm
                                                            [18] => Plucker
                                                            [19] => ReqwirelessWeb
                                                            [20] => SonyEricsson
                                                            [21] => Symbian
                                                            [22] => UP\.Browser
                                                            [23] => webOS
                                                            [24] => Windows CE
                                                            [25] => Windows Phone OS
                                                            [26] => Xiino
                                                        )

                                                )

                                            [requested] => Array
                                                (
                                                    [param] => requested
                                                    [value] => 1
                                                )

                                            [json] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/json
                                                        )

                                                    [param] => ext
                                                    [value] => json
                                                )

                                            [xml] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [param] => ext
                                                    [value] => xml
                                                )

                                        )

                                    [_input:protected] => 
                                )

                        )

                )

            [defaultPriority] => 10
        )

    [viewClass] => View
    [View] => 
    [ext] => .ctp
    [plugin] => 
    [cacheAction] => 
    [passedArgs] => Array
        (
            [0] => gene_id
            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
        )

    [scaffold] => 
    [methods] => Array
        (
            [0] => view_result
            [1] => custom_tree_creation
        )

    [modelClass] => Annotation
    [modelKey] => analysi
    [validationErrors] => 
    [_mergeParent:protected] => AppController
    [_eventManager:protected] => CakeEventManager Object
        (
            [_listeners:protected] => Array
                (
                    [Controller.initialize] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => beforeFilter
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                    [Controller.startup] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                    [Controller.beforeRender] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => beforeRender
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                    [Controller.beforeRedirect] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => beforeRedirect
                                                )

                                            [passParams] => 1
                                        )

                                )

                        )

                    [Controller.shutdown] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => afterFilter
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                )

            [_isGlobal:protected] => 
        )

    [Session] => SessionComponent Object
        (
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
 *RECURSION*
                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [DataUtils] => DataUtilsComponent Object
        (
            [name] => DataUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                    [1] => FunctionalUtils
                    [2] => GeneFamilies
                    [3] => GenomeBrowser
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
 *RECURSION*
                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                    [FunctionalUtils] => Array
                        (
                            [class] => FunctionalUtils
                            [settings] => Array
                                (
                                )

                        )

                    [GeneFamilies] => Array
                        (
                            [class] => GeneFamilies
                            [settings] => Array
                                (
                                )

                        )

                    [GenomeBrowser] => Array
                        (
                            [class] => GenomeBrowser
                            [settings] => Array
                                (
                                )

                        )

                )

            [GeneFamilies] => GeneFamiliesComponent Object
                (
                    [name] => GeneFamilies
                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                    [_Collection:protected] => ComponentCollection Object
                        (
                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                            [_enabled:protected] => Array
                                (
                                    [Session] => Array
                                        (
                                            [0] => 10
                                            [1] => 1
                                        )

                                    [DataUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 2
                                        )

                                    [FunctionalAnnotationUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 3
                                        )

                                    [GeneFamilies] => Array
                                        (
                                            [0] => 10
                                            [1] => 4
                                        )

                                    [Organism] => Array
                                        (
                                            [0] => 10
                                            [1] => 5
                                        )

                                    [Blast] => Array
                                        (
                                            [0] => 10
                                            [1] => 6
                                        )

                                    [WorkbenchUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 7
                                        )

                                    [PhylogeneticModuleUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 8
                                        )

                                    [ExternalPrograms] => Array
                                        (
                                            [0] => 10
                                            [1] => 9
                                        )

                                    [FastaUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 10
                                        )

                                    [MsaUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 11
                                        )

                                    [PhylogeneticUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 12
                                        )

                                    [Sequence] => Array
                                        (
                                            [0] => 10
                                            [1] => 13
                                        )

                                    [RequestHandler] => Array
                                        (
                                            [0] => 10
                                            [1] => 14
                                        )

                                )

                            [_loaded:protected] => Array
                                (
                                    [Session] => SessionComponent Object
                                        (
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [DataUtils] => DataUtilsComponent Object
 *RECURSION*
                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                        (
                                            [name] => FunctionalAnnotationUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => FunctionalUtils
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [FunctionalUtils] => Array
                                                        (
                                                            [class] => FunctionalUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
 *RECURSION*
                                    [Organism] => OrganismComponent Object
                                        (
                                            [name] => Organism
                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => GenomeBrowser
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [GenomeBrowser] => Array
                                                        (
                                                            [class] => GenomeBrowser
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [Blast] => BlastComponent Object
                                        (
                                            [name] => Blast
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                        (
                                            [name] => WorkbenchUtils
                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => ExternalPrograms
                                                    [1] => FormUtils
                                                    [2] => FunctionalUtils
                                                    [3] => GeneFamilies
                                                    [4] => WorkbenchSharedAccessRights
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [FormUtils] => Array
                                                        (
                                                            [class] => FormUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [FunctionalUtils] => Array
                                                        (
                                                            [class] => FunctionalUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [GeneFamilies] => Array
                                                        (
                                                            [class] => GeneFamilies
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [WorkbenchSharedAccessRights] => Array
                                                        (
                                                            [class] => WorkbenchSharedAccessRights
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                        (
                                            [name] => PhylogeneticModuleUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => ExternalPrograms
                                                    [1] => FastaUtils
                                                    [2] => MsaUtils
                                                    [3] => PhylogeneticUtils
                                                    [4] => Sequence
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [FastaUtils] => Array
                                                        (
                                                            [class] => FastaUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [MsaUtils] => Array
                                                        (
                                                            [class] => MsaUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [PhylogeneticUtils] => Array
                                                        (
                                                            [class] => PhylogeneticUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [Sequence] => Array
                                                        (
                                                            [class] => Sequence
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                        (
                                            [name] => ExternalPrograms
                                            [components] => Array
                                                (
                                                    [0] => FastaUtils
                                                )

                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                (
                                                    [java] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => java/x86_64/21.0.2
                                                                        )

                                                                    [command] => java -Djava.awt.headless=true
                                                                )

                                                            [local_settings] => java -Djava.awt.headless=true
                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                        )

                                                    [perl] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => perl
                                                                        )

                                                                    [command] => perl -w
                                                                )

                                                            [local_settings] => /usr/bin/perl
                                                        )

                                                    [bash] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                        )

                                                                    [command] => 
                                                                )

                                                            [local_settings] => 
                                                        )

                                                    [bedops] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => bedops/x86_64/2.4.37
                                                                        )

                                                                    [command] => 
                                                                )

                                                            [local_settings] => 
                                                        )

                                                    [blastdbcmd] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => blast
                                                                        )

                                                                    [command] => blastdbcmd
                                                                )

                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                        )

                                                    [blast] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => blast
                                                                        )

                                                                    [command] => 
                                                                )

                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                        )

                                                    [muscle] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => muscle/x86_64/3.8.31
                                                                        )

                                                                )

                                                        )

                                                    [mafft] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => mafft/x86_64/7.187
                                                                        )

                                                                )

                                                        )

                                                    [phyml] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => phyml/x86_64/20150219
                                                                        )

                                                                )

                                                        )

                                                    [fasttree] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => fasttree/x86_64/2.1.7
                                                                        )

                                                                )

                                                        )

                                                    [raxml] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => raxml/x86_64/8.2.8
                                                                        )

                                                                )

                                                        )

                                                    [iqtree] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => iqtree/x86_64/1.5.5
                                                                        )

                                                                )

                                                        )

                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [FastaUtils] => Array
                                                        (
                                                            [class] => FastaUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [FastaUtils] => FastaUtilsComponent Object
                                        (
                                            [name] => FastaUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [MsaUtils] => MsaUtilsComponent Object
                                        (
                                            [name] => MsaUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                        (
                                            [name] => PhylogeneticUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => ExternalPrograms
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [Sequence] => SequenceComponent Object
                                        (
                                            [name] => Sequence
                                            [components] => Array
                                                (
                                                    [0] => Blast
                                                    [1] => Coordinates
                                                    [2] => ExternalPrograms
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [Blast] => Array
                                                        (
                                                            [class] => Blast
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [Coordinates] => Array
                                                        (
                                                            [class] => Coordinates
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                            [controller] => AnalysisController Object
 *RECURSION*
                                        )

                                    [RequestHandler] => RequestHandlerComponent Object
                                        (
                                            [ajaxLayout] => ajax
                                            [enabled] => 1
                                            [request] => CakeRequest Object
                                                (
                                                    [params] => Array
                                                        (
                                                            [plugin] => 
                                                            [controller] => analysis
                                                            [action] => custom_tree_creation
                                                            [named] => Array
                                                                (
                                                                )

                                                            [pass] => Array
                                                                (
                                                                    [0] => gene_id
                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                )

                                                            [isAjax] => 
                                                        )

                                                    [data] => Array
                                                        (
                                                        )

                                                    [query] => Array
                                                        (
                                                        )

                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                    [_detectors:protected] => Array
                                                        (
                                                            [get] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => GET
                                                                )

                                                            [patch] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PATCH
                                                                )

                                                            [post] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => POST
                                                                )

                                                            [put] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PUT
                                                                )

                                                            [delete] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => DELETE
                                                                )

                                                            [head] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => HEAD
                                                                )

                                                            [options] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => OPTIONS
                                                                )

                                                            [ssl] => Array
                                                                (
                                                                    [env] => HTTPS
                                                                    [value] => 1
                                                                )

                                                            [ajax] => Array
                                                                (
                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                    [value] => XMLHttpRequest
                                                                )

                                                            [flash] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                )

                                                            [mobile] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [options] => Array
                                                                        (
                                                                            [0] => Android
                                                                            [1] => AvantGo
                                                                            [2] => BB10
                                                                            [3] => BlackBerry
                                                                            [4] => DoCoMo
                                                                            [5] => Fennec
                                                                            [6] => iPod
                                                                            [7] => iPhone
                                                                            [8] => iPad
                                                                            [9] => J2ME
                                                                            [10] => MIDP
                                                                            [11] => NetFront
                                                                            [12] => Nokia
                                                                            [13] => Opera Mini
                                                                            [14] => Opera Mobi
                                                                            [15] => PalmOS
                                                                            [16] => PalmSource
                                                                            [17] => portalmmm
                                                                            [18] => Plucker
                                                                            [19] => ReqwirelessWeb
                                                                            [20] => SonyEricsson
                                                                            [21] => Symbian
                                                                            [22] => UP\.Browser
                                                                            [23] => webOS
                                                                            [24] => Windows CE
                                                                            [25] => Windows Phone OS
                                                                            [26] => Xiino
                                                                        )

                                                                )

                                                            [requested] => Array
                                                                (
                                                                    [param] => requested
                                                                    [value] => 1
                                                                )

                                                            [json] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/json
                                                                        )

                                                                    [param] => ext
                                                                    [value] => json
                                                                )

                                                            [xml] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/xml
                                                                            [1] => text/xml
                                                                        )

                                                                    [param] => ext
                                                                    [value] => xml
                                                                )

                                                        )

                                                    [_input:protected] => 
                                                )

                                            [response] => CakeResponse Object
                                                (
                                                    [_statusCodes:protected] => Array
                                                        (
                                                            [100] => Continue
                                                            [101] => Switching Protocols
                                                            [200] => OK
                                                            [201] => Created
                                                            [202] => Accepted
                                                            [203] => Non-Authoritative Information
                                                            [204] => No Content
                                                            [205] => Reset Content
                                                            [206] => Partial Content
                                                            [300] => Multiple Choices
                                                            [301] => Moved Permanently
                                                            [302] => Found
                                                            [303] => See Other
                                                            [304] => Not Modified
                                                            [305] => Use Proxy
                                                            [307] => Temporary Redirect
                                                            [400] => Bad Request
                                                            [401] => Unauthorized
                                                            [402] => Payment Required
                                                            [403] => Forbidden
                                                            [404] => Not Found
                                                            [405] => Method Not Allowed
                                                            [406] => Not Acceptable
                                                            [407] => Proxy Authentication Required
                                                            [408] => Request Time-out
                                                            [409] => Conflict
                                                            [410] => Gone
                                                            [411] => Length Required
                                                            [412] => Precondition Failed
                                                            [413] => Request Entity Too Large
                                                            [414] => Request-URI Too Large
                                                            [415] => Unsupported Media Type
                                                            [416] => Requested range not satisfiable
                                                            [417] => Expectation Failed
                                                            [429] => Too Many Requests
                                                            [500] => Internal Server Error
                                                            [501] => Not Implemented
                                                            [502] => Bad Gateway
                                                            [503] => Service Unavailable
                                                            [504] => Gateway Time-out
                                                            [505] => Unsupported Version
                                                        )

                                                    [_mimeTypes:protected] => Array
                                                        (
                                                            [html] => Array
                                                                (
                                                                    [0] => text/html
                                                                    [1] => */*
                                                                )

                                                            [json] => application/json
                                                            [xml] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [rss] => application/rss+xml
                                                            [ai] => application/postscript
                                                            [bcpio] => application/x-bcpio
                                                            [bin] => application/octet-stream
                                                            [ccad] => application/clariscad
                                                            [cdf] => application/x-netcdf
                                                            [class] => application/octet-stream
                                                            [cpio] => application/x-cpio
                                                            [cpt] => application/mac-compactpro
                                                            [csh] => application/x-csh
                                                            [csv] => Array
                                                                (
                                                                    [0] => text/csv
                                                                    [1] => application/vnd.ms-excel
                                                                )

                                                            [dcr] => application/x-director
                                                            [dir] => application/x-director
                                                            [dms] => application/octet-stream
                                                            [doc] => application/msword
                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                            [drw] => application/drafting
                                                            [dvi] => application/x-dvi
                                                            [dwg] => application/acad
                                                            [dxf] => application/dxf
                                                            [dxr] => application/x-director
                                                            [eot] => application/vnd.ms-fontobject
                                                            [eps] => application/postscript
                                                            [exe] => application/octet-stream
                                                            [ez] => application/andrew-inset
                                                            [flv] => video/x-flv
                                                            [gtar] => application/x-gtar
                                                            [gz] => application/x-gzip
                                                            [bz2] => application/x-bzip
                                                            [7z] => application/x-7z-compressed
                                                            [hdf] => application/x-hdf
                                                            [hqx] => application/mac-binhex40
                                                            [ico] => image/x-icon
                                                            [ips] => application/x-ipscript
                                                            [ipx] => application/x-ipix
                                                            [js] => application/javascript
                                                            [jsonapi] => application/vnd.api+json
                                                            [latex] => application/x-latex
                                                            [lha] => application/octet-stream
                                                            [lsp] => application/x-lisp
                                                            [lzh] => application/octet-stream
                                                            [man] => application/x-troff-man
                                                            [me] => application/x-troff-me
                                                            [mif] => application/vnd.mif
                                                            [ms] => application/x-troff-ms
                                                            [nc] => application/x-netcdf
                                                            [oda] => application/oda
                                                            [otf] => font/otf
                                                            [pdf] => application/pdf
                                                            [pgn] => application/x-chess-pgn
                                                            [pot] => application/vnd.ms-powerpoint
                                                            [pps] => application/vnd.ms-powerpoint
                                                            [ppt] => application/vnd.ms-powerpoint
                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                            [ppz] => application/vnd.ms-powerpoint
                                                            [pre] => application/x-freelance
                                                            [prt] => application/pro_eng
                                                            [ps] => application/postscript
                                                            [roff] => application/x-troff
                                                            [scm] => application/x-lotusscreencam
                                                            [set] => application/set
                                                            [sh] => application/x-sh
                                                            [shar] => application/x-shar
                                                            [sit] => application/x-stuffit
                                                            [skd] => application/x-koan
                                                            [skm] => application/x-koan
                                                            [skp] => application/x-koan
                                                            [skt] => application/x-koan
                                                            [smi] => application/smil
                                                            [smil] => application/smil
                                                            [sol] => application/solids
                                                            [spl] => application/x-futuresplash
                                                            [src] => application/x-wais-source
                                                            [step] => application/STEP
                                                            [stl] => application/SLA
                                                            [stp] => application/STEP
                                                            [sv4cpio] => application/x-sv4cpio
                                                            [sv4crc] => application/x-sv4crc
                                                            [svg] => image/svg+xml
                                                            [svgz] => image/svg+xml
                                                            [swf] => application/x-shockwave-flash
                                                            [t] => application/x-troff
                                                            [tar] => application/x-tar
                                                            [tcl] => application/x-tcl
                                                            [tex] => application/x-tex
                                                            [texi] => application/x-texinfo
                                                            [texinfo] => application/x-texinfo
                                                            [tr] => application/x-troff
                                                            [tsp] => application/dsptype
                                                            [ttc] => font/ttf
                                                            [ttf] => font/ttf
                                                            [unv] => application/i-deas
                                                            [ustar] => application/x-ustar
                                                            [vcd] => application/x-cdlink
                                                            [vda] => application/vda
                                                            [xlc] => application/vnd.ms-excel
                                                            [xll] => application/vnd.ms-excel
                                                            [xlm] => application/vnd.ms-excel
                                                            [xls] => application/vnd.ms-excel
                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                            [xlw] => application/vnd.ms-excel
                                                            [zip] => application/zip
                                                            [aif] => audio/x-aiff
                                                            [aifc] => audio/x-aiff
                                                            [aiff] => audio/x-aiff
                                                            [au] => audio/basic
                                                            [kar] => audio/midi
                                                            [mid] => audio/midi
                                                            [midi] => audio/midi
                                                            [mp2] => audio/mpeg
                                                            [mp3] => audio/mpeg
                                                            [mpga] => audio/mpeg
                                                            [ogg] => audio/ogg
                                                            [oga] => audio/ogg
                                                            [spx] => audio/ogg
                                                            [ra] => audio/x-realaudio
                                                            [ram] => audio/x-pn-realaudio
                                                            [rm] => audio/x-pn-realaudio
                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                            [snd] => audio/basic
                                                            [tsi] => audio/TSP-audio
                                                            [wav] => audio/x-wav
                                                            [aac] => audio/aac
                                                            [asc] => text/plain
                                                            [c] => text/plain
                                                            [cc] => text/plain
                                                            [css] => text/css
                                                            [etx] => text/x-setext
                                                            [f] => text/plain
                                                            [f90] => text/plain
                                                            [h] => text/plain
                                                            [hh] => text/plain
                                                            [htm] => Array
                                                                (
                                                                    [0] => text/html
                                                                    [1] => */*
                                                                )

                                                            [ics] => text/calendar
                                                            [m] => text/plain
                                                            [rtf] => text/rtf
                                                            [rtx] => text/richtext
                                                            [sgm] => text/sgml
                                                            [sgml] => text/sgml
                                                            [tsv] => text/tab-separated-values
                                                            [tpl] => text/template
                                                            [txt] => text/plain
                                                            [text] => text/plain
                                                            [avi] => video/x-msvideo
                                                            [fli] => video/x-fli
                                                            [mov] => video/quicktime
                                                            [movie] => video/x-sgi-movie
                                                            [mpe] => video/mpeg
                                                            [mpeg] => video/mpeg
                                                            [mpg] => video/mpeg
                                                            [qt] => video/quicktime
                                                            [viv] => video/vnd.vivo
                                                            [vivo] => video/vnd.vivo
                                                            [ogv] => video/ogg
                                                            [webm] => video/webm
                                                            [mp4] => video/mp4
                                                            [m4v] => video/mp4
                                                            [f4v] => video/mp4
                                                            [f4p] => video/mp4
                                                            [m4a] => audio/mp4
                                                            [f4a] => audio/mp4
                                                            [f4b] => audio/mp4
                                                            [gif] => image/gif
                                                            [ief] => image/ief
                                                            [jpg] => image/jpeg
                                                            [jpeg] => image/jpeg
                                                            [jpe] => image/jpeg
                                                            [pbm] => image/x-portable-bitmap
                                                            [pgm] => image/x-portable-graymap
                                                            [png] => image/png
                                                            [pnm] => image/x-portable-anymap
                                                            [ppm] => image/x-portable-pixmap
                                                            [ras] => image/cmu-raster
                                                            [rgb] => image/x-rgb
                                                            [tif] => image/tiff
                                                            [tiff] => image/tiff
                                                            [xbm] => image/x-xbitmap
                                                            [xpm] => image/x-xpixmap
                                                            [xwd] => image/x-xwindowdump
                                                            [psd] => Array
                                                                (
                                                                    [0] => application/photoshop
                                                                    [1] => application/psd
                                                                    [2] => image/psd
                                                                    [3] => image/x-photoshop
                                                                    [4] => image/photoshop
                                                                    [5] => zz-application/zz-winassoc-psd
                                                                )

                                                            [ice] => x-conference/x-cooltalk
                                                            [iges] => model/iges
                                                            [igs] => model/iges
                                                            [mesh] => model/mesh
                                                            [msh] => model/mesh
                                                            [silo] => model/mesh
                                                            [vrml] => model/vrml
                                                            [wrl] => model/vrml
                                                            [mime] => www/mime
                                                            [pdb] => chemical/x-pdb
                                                            [xyz] => chemical/x-pdb
                                                            [javascript] => application/javascript
                                                            [form] => application/x-www-form-urlencoded
                                                            [file] => multipart/form-data
                                                            [xhtml] => Array
                                                                (
                                                                    [0] => application/xhtml+xml
                                                                    [1] => application/xhtml
                                                                    [2] => text/xhtml
                                                                )

                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                            [atom] => application/atom+xml
                                                            [amf] => application/x-amf
                                                            [wap] => Array
                                                                (
                                                                    [0] => text/vnd.wap.wml
                                                                    [1] => text/vnd.wap.wmlscript
                                                                    [2] => image/vnd.wap.wbmp
                                                                )

                                                            [wml] => text/vnd.wap.wml
                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                            [wbmp] => image/vnd.wap.wbmp
                                                            [woff] => application/x-font-woff
                                                            [webp] => image/webp
                                                            [appcache] => text/cache-manifest
                                                            [manifest] => text/cache-manifest
                                                            [htc] => text/x-component
                                                            [rdf] => application/xml
                                                            [crx] => application/x-chrome-extension
                                                            [oex] => application/x-opera-extension
                                                            [xpi] => application/x-xpinstall
                                                            [safariextz] => application/octet-stream
                                                            [webapp] => application/x-web-app-manifest+json
                                                            [vcf] => text/x-vcard
                                                            [vtt] => text/vtt
                                                            [mkv] => video/x-matroska
                                                            [pkpass] => application/vnd.apple.pkpass
                                                            [ajax] => text/html
                                                        )

                                                    [_protocol:protected] => HTTP/1.1
                                                    [_status:protected] => 200
                                                    [_contentType:protected] => text/html
                                                    [_headers:protected] => Array
                                                        (
                                                        )

                                                    [_body:protected] => 
                                                    [_file:protected] => 
                                                    [_fileRange:protected] => 
                                                    [_charset:protected] => UTF-8
                                                    [_cacheDirectives:protected] => Array
                                                        (
                                                        )

                                                    [_cookies:protected] => Array
                                                        (
                                                        )

                                                )

                                            [ext] => 
                                            [_renderType:protected] => 
                                            [_inputTypeMap:protected] => Array
                                                (
                                                    [json] => Array
                                                        (
                                                            [0] => json_decode
                                                            [1] => 1
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [0] => Array
                                                                (
                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                    [1] => convertXml
                                                                )

                                                        )

                                                )

                                            [_viewClassMap:protected] => Array
                                                (
                                                    [json] => Json
                                                    [xml] => Xml
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                    [checkHttpCache] => 1
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                            [params] => CakeRequest Object
                                                (
                                                    [params] => Array
                                                        (
                                                            [plugin] => 
                                                            [controller] => analysis
                                                            [action] => custom_tree_creation
                                                            [named] => Array
                                                                (
                                                                )

                                                            [pass] => Array
                                                                (
                                                                    [0] => gene_id
                                                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                                )

                                                            [isAjax] => 
                                                        )

                                                    [data] => Array
                                                        (
                                                        )

                                                    [query] => Array
                                                        (
                                                        )

                                                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                                    [_detectors:protected] => Array
                                                        (
                                                            [get] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => GET
                                                                )

                                                            [patch] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PATCH
                                                                )

                                                            [post] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => POST
                                                                )

                                                            [put] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PUT
                                                                )

                                                            [delete] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => DELETE
                                                                )

                                                            [head] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => HEAD
                                                                )

                                                            [options] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => OPTIONS
                                                                )

                                                            [ssl] => Array
                                                                (
                                                                    [env] => HTTPS
                                                                    [value] => 1
                                                                )

                                                            [ajax] => Array
                                                                (
                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                    [value] => XMLHttpRequest
                                                                )

                                                            [flash] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                )

                                                            [mobile] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [options] => Array
                                                                        (
                                                                            [0] => Android
                                                                            [1] => AvantGo
                                                                            [2] => BB10
                                                                            [3] => BlackBerry
                                                                            [4] => DoCoMo
                                                                            [5] => Fennec
                                                                            [6] => iPod
                                                                            [7] => iPhone
                                                                            [8] => iPad
                                                                            [9] => J2ME
                                                                            [10] => MIDP
                                                                            [11] => NetFront
                                                                            [12] => Nokia
                                                                            [13] => Opera Mini
                                                                            [14] => Opera Mobi
                                                                            [15] => PalmOS
                                                                            [16] => PalmSource
                                                                            [17] => portalmmm
                                                                            [18] => Plucker
                                                                            [19] => ReqwirelessWeb
                                                                            [20] => SonyEricsson
                                                                            [21] => Symbian
                                                                            [22] => UP\.Browser
                                                                            [23] => webOS
                                                                            [24] => Windows CE
                                                                            [25] => Windows Phone OS
                                                                            [26] => Xiino
                                                                        )

                                                                )

                                                            [requested] => Array
                                                                (
                                                                    [param] => requested
                                                                    [value] => 1
                                                                )

                                                            [json] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/json
                                                                        )

                                                                    [param] => ext
                                                                    [value] => json
                                                                )

                                                            [xml] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/xml
                                                                            [1] => text/xml
                                                                        )

                                                                    [param] => ext
                                                                    [value] => xml
                                                                )

                                                        )

                                                    [_input:protected] => 
                                                )

                                        )

                                )

                            [defaultPriority] => 10
                        )

                    [settings] => Array
                        (
                        )

                    [components] => Array
                        (
                        )

                    [_componentMap:protected] => Array
                        (
                        )

                )

        )

    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
        (
            [name] => FunctionalAnnotationUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => FunctionalUtils
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
 *RECURSION*
                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [FunctionalUtils] => Array
                        (
                            [class] => FunctionalUtils
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [GeneFamilies] => GeneFamiliesComponent Object
        (
            [name] => GeneFamilies
            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
 *RECURSION*
                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
 *RECURSION*
                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [Organism] => OrganismComponent Object
        (
            [name] => Organism
            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => GenomeBrowser
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
 *RECURSION*
                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [GenomeBrowser] => Array
                        (
                            [class] => GenomeBrowser
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [Blast] => BlastComponent Object
        (
            [name] => Blast
            [controller] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
 *RECURSION*
                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [WorkbenchUtils] => WorkbenchUtilsComponent Object
        (
            [name] => WorkbenchUtils
            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                    [1] => FormUtils
                    [2] => FunctionalUtils
                    [3] => GeneFamilies
                    [4] => WorkbenchSharedAccessRights
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
 *RECURSION*
                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                    [FormUtils] => Array
                        (
                            [class] => FormUtils
                            [settings] => Array
                                (
                                )

                        )

                    [FunctionalUtils] => Array
                        (
                            [class] => FunctionalUtils
                            [settings] => Array
                                (
                                )

                        )

                    [GeneFamilies] => Array
                        (
                            [class] => GeneFamilies
                            [settings] => Array
                                (
                                )

                        )

                    [WorkbenchSharedAccessRights] => Array
                        (
                            [class] => WorkbenchSharedAccessRights
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
        (
            [name] => PhylogeneticModuleUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                    [1] => FastaUtils
                    [2] => MsaUtils
                    [3] => PhylogeneticUtils
                    [4] => Sequence
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
 *RECURSION*
                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                    [FastaUtils] => Array
                        (
                            [class] => FastaUtils
                            [settings] => Array
                                (
                                )

                        )

                    [MsaUtils] => Array
                        (
                            [class] => MsaUtils
                            [settings] => Array
                                (
                                )

                        )

                    [PhylogeneticUtils] => Array
                        (
                            [class] => PhylogeneticUtils
                            [settings] => Array
                                (
                                )

                        )

                    [Sequence] => Array
                        (
                            [class] => Sequence
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [ExternalPrograms] => ExternalProgramsComponent Object
        (
            [name] => ExternalPrograms
            [components] => Array
                (
                    [0] => FastaUtils
                )

            [program_paths:ExternalProgramsComponent:private] => Array
                (
                    [java] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => java/x86_64/21.0.2
                                        )

                                    [command] => java -Djava.awt.headless=true
                                )

                            [local_settings] => java -Djava.awt.headless=true
                            [db_connector] => mysql-connector-java-8.0.21.jar
                        )

                    [perl] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => perl
                                        )

                                    [command] => perl -w
                                )

                            [local_settings] => /usr/bin/perl
                        )

                    [bash] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                        )

                                    [command] => 
                                )

                            [local_settings] => 
                        )

                    [bedops] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => bedops/x86_64/2.4.37
                                        )

                                    [command] => 
                                )

                            [local_settings] => 
                        )

                    [blastdbcmd] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => blast
                                        )

                                    [command] => blastdbcmd
                                )

                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                        )

                    [blast] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => blast
                                        )

                                    [command] => 
                                )

                            [local_settings] => /usr/local/blast/2.2.24/bin/
                        )

                    [muscle] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => muscle/x86_64/3.8.31
                                        )

                                )

                        )

                    [mafft] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => mafft/x86_64/7.187
                                        )

                                )

                        )

                    [phyml] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => phyml/x86_64/20150219
                                        )

                                )

                        )

                    [fasttree] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => fasttree/x86_64/2.1.7
                                        )

                                )

                        )

                    [raxml] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => raxml/x86_64/8.2.8
                                        )

                                )

                        )

                    [iqtree] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => iqtree/x86_64/1.5.5
                                        )

                                )

                        )

                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
 *RECURSION*
                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [FastaUtils] => Array
                        (
                            [class] => FastaUtils
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [FastaUtils] => FastaUtilsComponent Object
        (
            [name] => FastaUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
 *RECURSION*
                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [MsaUtils] => MsaUtilsComponent Object
        (
            [name] => MsaUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
 *RECURSION*
                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
        (
            [name] => PhylogeneticUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
 *RECURSION*
                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [Sequence] => SequenceComponent Object
        (
            [name] => Sequence
            [components] => Array
                (
                    [0] => Blast
                    [1] => Coordinates
                    [2] => ExternalPrograms
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
 *RECURSION*
                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [Blast] => Array
                        (
                            [class] => Blast
                            [settings] => Array
                                (
                                )

                        )

                    [Coordinates] => Array
                        (
                            [class] => Coordinates
                            [settings] => Array
                                (
                                )

                        )

                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                )

            [controller] => AnalysisController Object
 *RECURSION*
        )

    [RequestHandler] => RequestHandlerComponent Object
        (
            [ajaxLayout] => ajax
            [enabled] => 1
            [request] => CakeRequest Object
                (
                    [params] => Array
                        (
                            [plugin] => 
                            [controller] => analysis
                            [action] => custom_tree_creation
                            [named] => Array
                                (
                                )

                            [pass] => Array
                                (
                                    [0] => gene_id
                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                )

                            [isAjax] => 
                        )

                    [data] => Array
                        (
                        )

                    [query] => Array
                        (
                        )

                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                    [base] => /plaza.dev/_dev_instances/feedback
                    [webroot] => /plaza.dev/_dev_instances/feedback/
                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                    [_detectors:protected] => Array
                        (
                            [get] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => GET
                                )

                            [patch] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PATCH
                                )

                            [post] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => POST
                                )

                            [put] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PUT
                                )

                            [delete] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => DELETE
                                )

                            [head] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => HEAD
                                )

                            [options] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => OPTIONS
                                )

                            [ssl] => Array
                                (
                                    [env] => HTTPS
                                    [value] => 1
                                )

                            [ajax] => Array
                                (
                                    [env] => HTTP_X_REQUESTED_WITH
                                    [value] => XMLHttpRequest
                                )

                            [flash] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                )

                            [mobile] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [options] => Array
                                        (
                                            [0] => Android
                                            [1] => AvantGo
                                            [2] => BB10
                                            [3] => BlackBerry
                                            [4] => DoCoMo
                                            [5] => Fennec
                                            [6] => iPod
                                            [7] => iPhone
                                            [8] => iPad
                                            [9] => J2ME
                                            [10] => MIDP
                                            [11] => NetFront
                                            [12] => Nokia
                                            [13] => Opera Mini
                                            [14] => Opera Mobi
                                            [15] => PalmOS
                                            [16] => PalmSource
                                            [17] => portalmmm
                                            [18] => Plucker
                                            [19] => ReqwirelessWeb
                                            [20] => SonyEricsson
                                            [21] => Symbian
                                            [22] => UP\.Browser
                                            [23] => webOS
                                            [24] => Windows CE
                                            [25] => Windows Phone OS
                                            [26] => Xiino
                                        )

                                )

                            [requested] => Array
                                (
                                    [param] => requested
                                    [value] => 1
                                )

                            [json] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/json
                                        )

                                    [param] => ext
                                    [value] => json
                                )

                            [xml] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/xml
                                            [1] => text/xml
                                        )

                                    [param] => ext
                                    [value] => xml
                                )

                        )

                    [_input:protected] => 
                )

            [response] => CakeResponse Object
                (
                    [_statusCodes:protected] => Array
                        (
                            [100] => Continue
                            [101] => Switching Protocols
                            [200] => OK
                            [201] => Created
                            [202] => Accepted
                            [203] => Non-Authoritative Information
                            [204] => No Content
                            [205] => Reset Content
                            [206] => Partial Content
                            [300] => Multiple Choices
                            [301] => Moved Permanently
                            [302] => Found
                            [303] => See Other
                            [304] => Not Modified
                            [305] => Use Proxy
                            [307] => Temporary Redirect
                            [400] => Bad Request
                            [401] => Unauthorized
                            [402] => Payment Required
                            [403] => Forbidden
                            [404] => Not Found
                            [405] => Method Not Allowed
                            [406] => Not Acceptable
                            [407] => Proxy Authentication Required
                            [408] => Request Time-out
                            [409] => Conflict
                            [410] => Gone
                            [411] => Length Required
                            [412] => Precondition Failed
                            [413] => Request Entity Too Large
                            [414] => Request-URI Too Large
                            [415] => Unsupported Media Type
                            [416] => Requested range not satisfiable
                            [417] => Expectation Failed
                            [429] => Too Many Requests
                            [500] => Internal Server Error
                            [501] => Not Implemented
                            [502] => Bad Gateway
                            [503] => Service Unavailable
                            [504] => Gateway Time-out
                            [505] => Unsupported Version
                        )

                    [_mimeTypes:protected] => Array
                        (
                            [html] => Array
                                (
                                    [0] => text/html
                                    [1] => */*
                                )

                            [json] => application/json
                            [xml] => Array
                                (
                                    [0] => application/xml
                                    [1] => text/xml
                                )

                            [rss] => application/rss+xml
                            [ai] => application/postscript
                            [bcpio] => application/x-bcpio
                            [bin] => application/octet-stream
                            [ccad] => application/clariscad
                            [cdf] => application/x-netcdf
                            [class] => application/octet-stream
                            [cpio] => application/x-cpio
                            [cpt] => application/mac-compactpro
                            [csh] => application/x-csh
                            [csv] => Array
                                (
                                    [0] => text/csv
                                    [1] => application/vnd.ms-excel
                                )

                            [dcr] => application/x-director
                            [dir] => application/x-director
                            [dms] => application/octet-stream
                            [doc] => application/msword
                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                            [drw] => application/drafting
                            [dvi] => application/x-dvi
                            [dwg] => application/acad
                            [dxf] => application/dxf
                            [dxr] => application/x-director
                            [eot] => application/vnd.ms-fontobject
                            [eps] => application/postscript
                            [exe] => application/octet-stream
                            [ez] => application/andrew-inset
                            [flv] => video/x-flv
                            [gtar] => application/x-gtar
                            [gz] => application/x-gzip
                            [bz2] => application/x-bzip
                            [7z] => application/x-7z-compressed
                            [hdf] => application/x-hdf
                            [hqx] => application/mac-binhex40
                            [ico] => image/x-icon
                            [ips] => application/x-ipscript
                            [ipx] => application/x-ipix
                            [js] => application/javascript
                            [jsonapi] => application/vnd.api+json
                            [latex] => application/x-latex
                            [lha] => application/octet-stream
                            [lsp] => application/x-lisp
                            [lzh] => application/octet-stream
                            [man] => application/x-troff-man
                            [me] => application/x-troff-me
                            [mif] => application/vnd.mif
                            [ms] => application/x-troff-ms
                            [nc] => application/x-netcdf
                            [oda] => application/oda
                            [otf] => font/otf
                            [pdf] => application/pdf
                            [pgn] => application/x-chess-pgn
                            [pot] => application/vnd.ms-powerpoint
                            [pps] => application/vnd.ms-powerpoint
                            [ppt] => application/vnd.ms-powerpoint
                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                            [ppz] => application/vnd.ms-powerpoint
                            [pre] => application/x-freelance
                            [prt] => application/pro_eng
                            [ps] => application/postscript
                            [roff] => application/x-troff
                            [scm] => application/x-lotusscreencam
                            [set] => application/set
                            [sh] => application/x-sh
                            [shar] => application/x-shar
                            [sit] => application/x-stuffit
                            [skd] => application/x-koan
                            [skm] => application/x-koan
                            [skp] => application/x-koan
                            [skt] => application/x-koan
                            [smi] => application/smil
                            [smil] => application/smil
                            [sol] => application/solids
                            [spl] => application/x-futuresplash
                            [src] => application/x-wais-source
                            [step] => application/STEP
                            [stl] => application/SLA
                            [stp] => application/STEP
                            [sv4cpio] => application/x-sv4cpio
                            [sv4crc] => application/x-sv4crc
                            [svg] => image/svg+xml
                            [svgz] => image/svg+xml
                            [swf] => application/x-shockwave-flash
                            [t] => application/x-troff
                            [tar] => application/x-tar
                            [tcl] => application/x-tcl
                            [tex] => application/x-tex
                            [texi] => application/x-texinfo
                            [texinfo] => application/x-texinfo
                            [tr] => application/x-troff
                            [tsp] => application/dsptype
                            [ttc] => font/ttf
                            [ttf] => font/ttf
                            [unv] => application/i-deas
                            [ustar] => application/x-ustar
                            [vcd] => application/x-cdlink
                            [vda] => application/vda
                            [xlc] => application/vnd.ms-excel
                            [xll] => application/vnd.ms-excel
                            [xlm] => application/vnd.ms-excel
                            [xls] => application/vnd.ms-excel
                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                            [xlw] => application/vnd.ms-excel
                            [zip] => application/zip
                            [aif] => audio/x-aiff
                            [aifc] => audio/x-aiff
                            [aiff] => audio/x-aiff
                            [au] => audio/basic
                            [kar] => audio/midi
                            [mid] => audio/midi
                            [midi] => audio/midi
                            [mp2] => audio/mpeg
                            [mp3] => audio/mpeg
                            [mpga] => audio/mpeg
                            [ogg] => audio/ogg
                            [oga] => audio/ogg
                            [spx] => audio/ogg
                            [ra] => audio/x-realaudio
                            [ram] => audio/x-pn-realaudio
                            [rm] => audio/x-pn-realaudio
                            [rpm] => audio/x-pn-realaudio-plugin
                            [snd] => audio/basic
                            [tsi] => audio/TSP-audio
                            [wav] => audio/x-wav
                            [aac] => audio/aac
                            [asc] => text/plain
                            [c] => text/plain
                            [cc] => text/plain
                            [css] => text/css
                            [etx] => text/x-setext
                            [f] => text/plain
                            [f90] => text/plain
                            [h] => text/plain
                            [hh] => text/plain
                            [htm] => Array
                                (
                                    [0] => text/html
                                    [1] => */*
                                )

                            [ics] => text/calendar
                            [m] => text/plain
                            [rtf] => text/rtf
                            [rtx] => text/richtext
                            [sgm] => text/sgml
                            [sgml] => text/sgml
                            [tsv] => text/tab-separated-values
                            [tpl] => text/template
                            [txt] => text/plain
                            [text] => text/plain
                            [avi] => video/x-msvideo
                            [fli] => video/x-fli
                            [mov] => video/quicktime
                            [movie] => video/x-sgi-movie
                            [mpe] => video/mpeg
                            [mpeg] => video/mpeg
                            [mpg] => video/mpeg
                            [qt] => video/quicktime
                            [viv] => video/vnd.vivo
                            [vivo] => video/vnd.vivo
                            [ogv] => video/ogg
                            [webm] => video/webm
                            [mp4] => video/mp4
                            [m4v] => video/mp4
                            [f4v] => video/mp4
                            [f4p] => video/mp4
                            [m4a] => audio/mp4
                            [f4a] => audio/mp4
                            [f4b] => audio/mp4
                            [gif] => image/gif
                            [ief] => image/ief
                            [jpg] => image/jpeg
                            [jpeg] => image/jpeg
                            [jpe] => image/jpeg
                            [pbm] => image/x-portable-bitmap
                            [pgm] => image/x-portable-graymap
                            [png] => image/png
                            [pnm] => image/x-portable-anymap
                            [ppm] => image/x-portable-pixmap
                            [ras] => image/cmu-raster
                            [rgb] => image/x-rgb
                            [tif] => image/tiff
                            [tiff] => image/tiff
                            [xbm] => image/x-xbitmap
                            [xpm] => image/x-xpixmap
                            [xwd] => image/x-xwindowdump
                            [psd] => Array
                                (
                                    [0] => application/photoshop
                                    [1] => application/psd
                                    [2] => image/psd
                                    [3] => image/x-photoshop
                                    [4] => image/photoshop
                                    [5] => zz-application/zz-winassoc-psd
                                )

                            [ice] => x-conference/x-cooltalk
                            [iges] => model/iges
                            [igs] => model/iges
                            [mesh] => model/mesh
                            [msh] => model/mesh
                            [silo] => model/mesh
                            [vrml] => model/vrml
                            [wrl] => model/vrml
                            [mime] => www/mime
                            [pdb] => chemical/x-pdb
                            [xyz] => chemical/x-pdb
                            [javascript] => application/javascript
                            [form] => application/x-www-form-urlencoded
                            [file] => multipart/form-data
                            [xhtml] => Array
                                (
                                    [0] => application/xhtml+xml
                                    [1] => application/xhtml
                                    [2] => text/xhtml
                                )

                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                            [atom] => application/atom+xml
                            [amf] => application/x-amf
                            [wap] => Array
                                (
                                    [0] => text/vnd.wap.wml
                                    [1] => text/vnd.wap.wmlscript
                                    [2] => image/vnd.wap.wbmp
                                )

                            [wml] => text/vnd.wap.wml
                            [wmlscript] => text/vnd.wap.wmlscript
                            [wbmp] => image/vnd.wap.wbmp
                            [woff] => application/x-font-woff
                            [webp] => image/webp
                            [appcache] => text/cache-manifest
                            [manifest] => text/cache-manifest
                            [htc] => text/x-component
                            [rdf] => application/xml
                            [crx] => application/x-chrome-extension
                            [oex] => application/x-opera-extension
                            [xpi] => application/x-xpinstall
                            [safariextz] => application/octet-stream
                            [webapp] => application/x-web-app-manifest+json
                            [vcf] => text/x-vcard
                            [vtt] => text/vtt
                            [mkv] => video/x-matroska
                            [pkpass] => application/vnd.apple.pkpass
                            [ajax] => text/html
                        )

                    [_protocol:protected] => HTTP/1.1
                    [_status:protected] => 200
                    [_contentType:protected] => text/html
                    [_headers:protected] => Array
                        (
                        )

                    [_body:protected] => 
                    [_file:protected] => 
                    [_fileRange:protected] => 
                    [_charset:protected] => UTF-8
                    [_cacheDirectives:protected] => Array
                        (
                        )

                    [_cookies:protected] => Array
                        (
                        )

                )

            [ext] => 
            [_renderType:protected] => 
            [_inputTypeMap:protected] => Array
                (
                    [json] => Array
                        (
                            [0] => json_decode
                            [1] => 1
                        )

                    [xml] => Array
                        (
                            [0] => Array
                                (
                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                    [1] => convertXml
                                )

                        )

                )

            [_viewClassMap:protected] => Array
                (
                    [json] => Json
                    [xml] => Xml
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
 *RECURSION*
                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                    [checkHttpCache] => 1
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

            [params] => CakeRequest Object
                (
                    [params] => Array
                        (
                            [plugin] => 
                            [controller] => analysis
                            [action] => custom_tree_creation
                            [named] => Array
                                (
                                )

                            [pass] => Array
                                (
                                    [0] => gene_id
                                    [1] => arahy.Tifrunner.gnm1.ann1.87PAU8
                                )

                            [isAjax] => 
                        )

                    [data] => Array
                        (
                        )

                    [query] => Array
                        (
                        )

                    [url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                    [base] => /plaza.dev/_dev_instances/feedback
                    [webroot] => /plaza.dev/_dev_instances/feedback/
                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
                    [_detectors:protected] => Array
                        (
                            [get] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => GET
                                )

                            [patch] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PATCH
                                )

                            [post] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => POST
                                )

                            [put] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PUT
                                )

                            [delete] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => DELETE
                                )

                            [head] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => HEAD
                                )

                            [options] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => OPTIONS
                                )

                            [ssl] => Array
                                (
                                    [env] => HTTPS
                                    [value] => 1
                                )

                            [ajax] => Array
                                (
                                    [env] => HTTP_X_REQUESTED_WITH
                                    [value] => XMLHttpRequest
                                )

                            [flash] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                )

                            [mobile] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [options] => Array
                                        (
                                            [0] => Android
                                            [1] => AvantGo
                                            [2] => BB10
                                            [3] => BlackBerry
                                            [4] => DoCoMo
                                            [5] => Fennec
                                            [6] => iPod
                                            [7] => iPhone
                                            [8] => iPad
                                            [9] => J2ME
                                            [10] => MIDP
                                            [11] => NetFront
                                            [12] => Nokia
                                            [13] => Opera Mini
                                            [14] => Opera Mobi
                                            [15] => PalmOS
                                            [16] => PalmSource
                                            [17] => portalmmm
                                            [18] => Plucker
                                            [19] => ReqwirelessWeb
                                            [20] => SonyEricsson
                                            [21] => Symbian
                                            [22] => UP\.Browser
                                            [23] => webOS
                                            [24] => Windows CE
                                            [25] => Windows Phone OS
                                            [26] => Xiino
                                        )

                                )

                            [requested] => Array
                                (
                                    [param] => requested
                                    [value] => 1
                                )

                            [json] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/json
                                        )

                                    [param] => ext
                                    [value] => json
                                )

                            [xml] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/xml
                                            [1] => text/xml
                                        )

                                    [param] => ext
                                    [value] => xml
                                )

                        )

                    [_input:protected] => 
                )

        )

    [Annotation] => Annotation Object
        (
            [name] => Annotation
            [useTable] => annotation
            [primaryKey] => gene_id
            [cacheQueries] => 
            [cacheSources] => 
            [belongsTo] => Array
                (
                    [AnnotSource] => Array
                        (
                            [foreignKey] => species
                            [className] => AnnotSource
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [counterCache] => 
                        )

                )

            [hasMany] => Array
                (
                    [GfDatum] => Array
                        (
                            [foreignKey] => gene_id
                            [className] => GfDatum
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [limit] => 
                            [offset] => 
                            [dependent] => 
                            [exclusive] => 
                            [finderQuery] => 
                            [counterQuery] => 
                        )

                )

            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => annotation
            [_schema:protected] => Array
                (
                    [gene_id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [transcript] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 100
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [coord_cds] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [start] => Array
                        (
                            [type] => integer
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                    [stop] => Array
                        (
                            [type] => integer
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                    [coord_transcript] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [seq] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [strand] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 1
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [chr] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 100
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [type] => Array
                        (
                            [type] => enum('coding','rna','te','pseudo')
                            [null] => 
                            [default] => coding
                            [length] => 6
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [check_transcript] => Array
                        (
                            [type] => enum('none','ne','eq')
                            [null] => 
                            [default] => none
                            [length] => 4
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [check_protein] => Array
                        (
                            [type] => enum('none','ne','eq')
                            [null] => 
                            [default] => none
                            [length] => 4
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [transl_table] => Array
                        (
                            [type] => tinyinteger
                            [null] => 
                            [default] => 1
                            [length] => 
                            [unsigned] => 
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => Annotation
            [tableToModel] => Array
                (
                    [annotation] => Annotation
                )

            [hasOne] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Annotation
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [Configuration] => Configuration Object
        (
            [name] => Configuration
            [useTable] => configuration
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => configuration
            [primaryKey] => id
            [_schema:protected] => Array
                (
                    [method] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 100
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [key] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 255
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [value] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [comment] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => Configuration
            [tableToModel] => Array
                (
                    [configuration] => Configuration
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Configuration
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [AnnotSource] => AnnotSource Object
        (
            [name] => AnnotSource
            [useTable] => annot_sources
            [primaryKey] => species
            [displayField] => common_name
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => annot_sources
            [_schema:protected] => Array
                (
                    [source] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 255
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [url] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 250
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [common_name] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 100
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [eco_type] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 100
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [description] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [paper] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [pubmed_id] => Array
                        (
                            [type] => integer
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [tax_id] => Array
                        (
                            [type] => integer
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                    [mitochondrion] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 15
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [chloroplast] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 15
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [disclaimer] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => AnnotSource
            [tableToModel] => Array
                (
                    [annot_sources] => AnnotSource
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => AnnotSource
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [GeneFamilyTypes] => GeneFamilyTypes Object
        (
            [name] => GeneFamilyTypes
            [useTable] => gene_family_types
            [primaryKey] => id
            [displayField] => name
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => gene_family_types
            [_schema:protected] => Array
                (
                    [id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 10
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [comment] => unique identifier for this gene family type. foreign key to other GF tables
                            [charset] => latin1
                        )

                    [name] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [collate] => latin1_swedish_ci
                            [comment] => description of gene family type
                            [charset] => latin1
                        )

                    [prefix] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 10
                            [collate] => latin1_swedish_ci
                            [comment] => prefix used for building the gf type. for compatibility reasons. shouldn't be used.
                            [charset] => latin1
                        )

                    [gene_type] => Array
                        (
                            [type] => enum('coding','rna','pseudo','te')
                            [null] => 
                            [default] => coding
                            [length] => 6
                            [collate] => latin1_swedish_ci
                            [comment] => should match type from table annotation
                            [charset] => latin1
                        )

                    [method] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 500
                            [collate] => latin1_swedish_ci
                            [comment] => JSON style information of the building method+parameters used
                            [charset] => latin1
                        )

                    [ancestry] => Array
                        (
                            [type] => enum('homology','orthology','homeology','other')
                            [null] => 
                            [default] => homology
                            [length] => 9
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [comment] => type of gene family content
                            [charset] => latin1
                        )

                    [parent_id] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 10
                            [collate] => latin1_swedish_ci
                            [comment] => link to the parent id if appropriate
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => GeneFamilyTypes
            [tableToModel] => Array
                (
                    [gene_family_types] => GeneFamilyTypes
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => GeneFamilyTypes
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [Similarities] => Similarities Object
        (
            [name] => Similarities
            [useTable] => similarities
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => similarities
            [primaryKey] => id
            [_schema:protected] => Array
                (
                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [query] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [hits] => Array
                        (
                            [type] => binary
                            [null] => 
                            [default] => 
                            [length] => 
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => Similarities
            [tableToModel] => Array
                (
                    [similarities] => Similarities
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Similarities
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [GfDatum] => GfDatum Object
        (
            [name] => GfDatum
            [useTable] => gf_data
            [belongsTo] => Array
                (
                    [Annotation] => Array
                        (
                            [className] => Annotation
                            [foreignKey] => gene_id
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [counterCache] => 
                        )

                    [Genefamily] => Array
                        (
                            [className] => GeneFamily
                            [foreignKey] => gf_id
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [counterCache] => 
                        )

                )

            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => gf_data
            [primaryKey] => id
            [_schema:protected] => Array
                (
                    [gf_id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [gf_type] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 10
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [comment] => links to gene_family_types id
                            [charset] => latin1
                        )

                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [gene_id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [synteny_data] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [cluster_data] => Array
                        (
                            [type] => float
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [outlier] => Array
                        (
                            [type] => smallinteger
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => GfDatum
            [tableToModel] => Array
                (
                    [gf_data] => GfDatum
                )

            [cacheQueries] => 
            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => GfDatum
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

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            [_eventManager:protected] => CakeEventManager Object
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            [_validator:protected] => 
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    [AdExperiments] => AdExperiments Object
        (
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            [useTable] => ad_experiments
            [primaryKey] => exp_id
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => ad_experiments
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                        (
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                            [collate] => latin1_swedish_ci
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                        )

                    [description_advanced] => Array
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                            [type] => text
                            [null] => 1
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                            [length] => 
                            [collate] => latin1_swedish_ci
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                    [organisms] => Array
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                            [type] => string
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                            [default] => 
                            [length] => 512
                            [collate] => latin1_swedish_ci
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                    [to_show] => Array
                        (
                            [type] => enum('true','false')
                            [null] => 
                            [default] => false
                            [length] => 5
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
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            [alias] => AdExperiments
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                (
                    [ad_experiments] => AdExperiments
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            [cacheQueries] => 
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                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
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                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
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            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
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                            [5] => dependent
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                    [hasMany] => Array
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                            [0] => className
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                            [6] => offset
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                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
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                    [hasAndBelongsToMany] => Array
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                            [0] => className
                            [1] => joinTable
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                            [4] => associationForeignKey
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                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
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                )

            [_associations:protected] => Array
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                    [2] => hasMany
                    [3] => hasAndBelongsToMany
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            [__backAssociation] => Array
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                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
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            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
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                                    [10] => Array
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                                                                    [_mappedMethods:protected] => Array
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                                                                    [defaultPriority] => 10
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                                                            [1] => trigger
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                                            [1] => Array
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                                                                    [_mappedMethods:protected] => Array
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                                                                    [_mappedMethods:protected] => Array
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                                                                    [_mappedMethods:protected] => Array
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                                            [1] => Array
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                                                    [passParams] => 1
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                                )

                            [Model.afterDelete] => Array
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                                    [10] => Array
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                                            [0] => Array
                                                (
                                                    [callable] => Array
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                                                            [0] => BehaviorCollection Object
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                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
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                                                            [1] => trigger
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                                            [1] => Array
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                                                    [passParams] => 
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                                        )

                                )

                        )

                    [_isGlobal:protected] => 
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            [_validator:protected] => 
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    [FunctionalClustersExperiments] => FunctionalClustersExperiments Object
        (
            [name] => FunctionalClustersExperiments
            [useTable] => functional_clusters_experiments
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => functional_clusters_experiments
            [primaryKey] => id
            [_schema:protected] => Array
                (
                    [exp_id] => Array
                        (
                            [type] => tinyinteger
                            [null] => 
                            [default] => 
                            [length] => 
                            [unsigned] => 
                            [key] => primary
                        )

                    [data_type] => Array
                        (
                            [type] => enum('GO','InterPro','MapMan')
                            [null] => 
                            [default] => 
                            [length] => 8
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [extra] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 30
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [min_genes_cluster] => Array
                        (
                            [type] => integer
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [max_genes_cluster] => Array
                        (
                            [type] => integer
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [max_cluster_size] => Array
                        (
                            [type] => integer
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [e-value] => Array
                        (
                            [type] => float
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [cluster_overlap] => Array
                        (
                            [type] => integer
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [has_tandems] => Array
                        (
                            [type] => boolean
                            [null] => 1
                            [default] => 
                            [length] => 1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => FunctionalClustersExperiments
            [tableToModel] => Array
                (
                    [functional_clusters_experiments] => FunctionalClustersExperiments
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => FunctionalClustersExperiments
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => FunctionalClustersExperiments
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => FunctionalClustersExperiments Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [Msa] => Msa Object
        (
            [name] => Msa
            [useTable] => msa
            [primaryKey] => msa_id
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => 
            [table] => msa
            [_schema:protected] => 
            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [plugin] => 
            [alias] => Msa
            [tableToModel] => Array
                (
                    [msa] => Msa
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Msa
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => 
            [_validator:protected] => 
        )

    [Trees] => Trees Object
        (
            [name] => Trees
            [useTable] => trees
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => 
            [table] => trees
            [primaryKey] => id
            [_schema:protected] => 
            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [plugin] => 
            [alias] => Trees
            [tableToModel] => Array
                (
                    [trees] => Trees
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Trees
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => 
            [_validator:protected] => 
        )

)
controller
Notice (8): Trying to get property 'Configuration' of non-object [APP/Controller/Component/GenomeBrowserComponent.php, line 105]
Errors

Call to a member function getBasicSpeciesTree() on null

Error: An Internal Error Has Occurred.

Stack Trace

  • APP/Controller/Component/DataUtilsComponent.php line 65GenomeBrowserComponent->getValidatedDataSettings()
  • APP/Controller/AppController.php line 94DataUtilsComponent->getSidebarToolsInfo()
  • CORE/Cake/Event/CakeEventManager.php line 243AppController->beforeRender()
  • CORE/Cake/Controller/Controller.php line 936CakeEventManager->dispatch()
  • CORE/Cake/Routing/Dispatcher.php line 200Controller->render()
  • CORE/Cake/Routing/Dispatcher.php line 167Dispatcher->_invoke()
  • APP/webroot/index.php line 151Dispatcher->dispatch()