Construction settings
Setting for the tools used to generate the platform (in alphabetical order). Links to either the official website or to the relevant publication are provided.
Gene family construction settings
TribeMCL
Source: Official website
- mclblastline
- I = 2
- scheme = 4
- other parameters are left on their default values
Phylogeny construction settings
Colinearity construction settings
i-ADHoRe 2.x
Source: Official website i-ADHoRe 2.0
- alignment_method: gg
- gap_size: 30
- cluster_gap: 35
- q_value: 0.85
- prob_cutoff: 0.01
- anchor_points: 5
- level_2_only: false
i-ADHoRe 3.0
Source: Official website i-ADHoRe 3.0
- alignment_method: gg
- gap_size: 30
- cluster_gap: 35
- q_value: 0.85
- prob_cutoff: 0.01
- anchor_points: 5
- level_2_only: false
i-ADHoRe 3.0
Source: Official website i-ADHoRe 3.0
- alignment_method: gg2
- gap_size: 30
- cluster_gap: 35
- q_value: 0.85
- prob_cutoff: 0.01
- anchor_points: 5
- level_2_only: true
PAML
Source: Official website
- verbose: 0
- noisy: 0
- runmode: -2
- seqtype: 1
- model: 0
- NSsites: 0
- icode: 0
- fix_alpha: 0
- fix_kappa: 0
- RateAncestor: 0
- CodonFreq: 2
Functional construction settings
C-Hunter
Reference : Yi et al.
Source: Official website
Multiple experiments can be performed per PLAZA instance, depending on a combination of the following settings/options
- Data type (e.g. GO, InterPro)
- Collapsing of tandem genes to the tandem representative (yes/no)
- Minimum/maximum size of cluster
- Minimum/maximum number of functionally related genes within a cluster
- E-value cut-off