Tools & parameters

DIAMOND

Fast and sensitive protein alignment using DIAMOND
Buchfink, B., Xie, C., & Huson, D. H
Nature methods 12.1 (2015): 59

Source: GitHub
Website: Official website

• Version: 0.9.18
• Parameters/command-line: --evalue 1e-5 [default], --more-sensitive

Infernal

Infernal 1.1: 100-fold faster RNA homology searches
Nawrocki, E. P., & Eddy, S. R.
Bioinformatics 29.22 (2013): 2933-2935

Source: GitHub
Website: Official website

• Version: 1.1.2
• Parameters/command-line: cmsearch using user-selected clans, --nohmmonly, --rfam, --cut_ga

Kaiju

Fast and sensitive taxonomic classification for metagenomics with Kaiju
Menzel, P., Ng, K. L., & Krogh, A.
Nature communications 7.1 (2016)

Source: GitHub
Website: Official website

• Version: 1.7.3
• Parameters/command-line: MEM mode, minimum match length 11, filter low complexity sequences

eggNOG-mapper

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., Von Mering, C., & Bork, P.
Molecular biology and evolution 34.8 (2017)

Source: GitHub
Website: Web server

• Version: 1.0.3-3-g3e22728
• Parameters/command-line: user-selected taxonomic scope, skipping DIAMOND search (run prior to calling eggNOG-mapper)

NCBI BLAST non-redundant protein database

Website: NCBI FTP

• Version: 2019-09-05
• Used as database for Kaiju.
  Contains 218,930,306 sequences from eukaryotes, bacteria, archaea, and viruses.

NCBI taxonomy

The NCBI Taxonomy database
Federhen, S.
Nucleic acids research 40.D1 (2012): D136-D143

Website: NCBI FTP

• Version: 2019-09-05

Rfam

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
Kalvari, I., Argasinska, J., Quinones-Olvera, N., Nawrocki, E. P., Rivas, E., Eddy, S. R., ... & Petrov, A. I.
Nucleic acids research 46.D1 (2018): D335-D342

Website: Official website

• Version: 14.1 (January 2019)
• Transcript sequences assigned to an RNA family are subsequently annotated with manually curated GO terms associated to the family, defined by Rfam curators.

MAFFT

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M.
Molecular biology and evolution 30.4 (2013): 772-780.

Source: Official website

• Version: 7.187
• Parameters/command-line: mafft --maxiterate 1000 --auto $fasta_file_path > $msa_file_path 2> $msa_file_path.log
• When creating a phylogenetic tree, optional editing of the alignment is performed using one of the available editing mode: removal of lowly conserved positions by trimming the sequences, filtering of partial sequences, or a combination of both

MUSCLE

MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C.
Nucleic acids research 32.5 (2004): 1792-1797

Source: Official website

• Version: 3.8.31
• Parameters/command-line: muscle -in $fasta_file_path -out $msa_file_path
• When creating a phylogenetic tree, optional editing of the alignment is performed using one of the available editing mode: removal of lowly conserved positions by trimming the sequences, filtering of partial sequences, or a combination of both

FastTree2

FastTree 2-approximately maximum-likelihood trees for large alignments
Price, M. N., Dehal, P. S., & Arkin, A. P.
PloS one 5, no. 3 (2010)

Source: FastTree website

• Version: 2.1.7
• Parameters/command-line: FastTree -wag -gamma $MSA_FILE_PATH > $NEWICK_FILE_PATH

IQ-TREE

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q.
Molecular biology and evolution 32.1 (2015): 268-274

Source: GitHub
Website: Official website

• Version: 1.7.0b7
• Parameters/command-line: iqtree -st AA -s $msa_stripped_file_path -pre $tmp_tree_file_path -nt 1 -bb 1000 -mset JTT,LG,WAG,Blosum62,VT,Dayhoff -mfreq F -mrate R > $tmp_tree_file_path.log

RaxML

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A.
Bioinformatics 30.9 (2014): 1312-1313.

Source: GitHub
Website: Official website

• Version: 8.2.8
• Parameters/command-line: raxmlHPC-PTHREADS-SSE3 -T 1 -f a -x 12345677 -p 12345677 -N 100 -m PROTGAMMAWAG -s $MSA_FILE_PATH -w $OUTPUT_DIR -n $NEWICK_FILE_NAME -k

PhyML

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O.
Systematic biology 59.3 (2010): 307-321.

Source: ATGC Montpellier website

• Version: 2015-02-19
• Parameters/command-line: phyml -i $msa_phylip_file_path -d aa -n 1 -b 100 -m WAG -f e -c 4 -a e -o n

Unipept standalone visualizations

Source: GitHub
Website: Unipept website

• Version: 1.7.2

KronaTools

Interactive metagenomic visualization in a Web browser
Ondov, B. D., Bergman, N. H., & Phillippy, A. M.
BMC bioinformatics 12.1 (2011): 385

Source: GitHub
Website: GitHub wiki

• Version: 2.7

MSAviewer

MSAViewer: interactive JavaScript visualization of multiple sequence alignments
Yachdav, G., Wilzbach, S., Rauscher, B., Sheridan, R., Sillitoe, I., Procter, J., ... & Goldberg, T.
Bioinformatics 32.22 (2016): 3501-3503

Source: GitHub
Website: BioJS page

• Version: 1.0.0

PhyD3

PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization.
Kreft, L., Botzki, A., Coppens, F., Vandepoele, K., & Van Bel, M.
Bioinformatics 33.18 (2017): 2946-2947

Source: GitHub
Website: Official website

• Version: 1.3