Table 1.
Software tools features for Ortholog studies since 2011 at 2017.
| Tool | Main Features | Platform | Implementation | Disponibility | Year of release |
|---|---|---|---|---|---|
| Hieranoid | Combines an efficient graph-based methodology with aspects of compute-intensive tree-based methods to infer orthology | Linux/Unix; web-server | Perl, BioPerl, BLAST, Muscle and Kalign | http://hieranoid.sbc.su.se/ | 2013 |
| MorFeus | Calculates a network score to the resulting network orthologs to find remotely stored orthologs proteins | Linux/Unix; web-server: | Python, biopython, networkx, gnuplot and BLAST+ | https://omictools.com/morfeus-tool | 2014 |
| OrthAgogue | High speed of the homology relationships in large data sets | Linux/Unix | BLAST, cmph and TBB | https://code.google.com/p/orthagogue/ | 2013 |
| OrthoInspector | Agile detection of orthology and in-paralogy incorporing a unique algorithm | Cross-platform (Java) | BLASTP+ package, JAVA, MySQL | http://www.lbgi.fr/orthoinspector/ | 2011 |
| OrthoFinder | Solves the fundamental biases in whole genome comparisons and improves inference accuracy in ortholog groups | Linux/Unix | BLASTP+ package, python, MCL graph clustering algorithm, MAFF and Fastree | http://www.stevekellylab.com/software/orthofinder | 2015 |
| Ortholog-Finder | Identifies genuine orthologs among distantly related species by phylogenetic analysis using ORF data | Linux/Unix | BLAST+, MAFFT, BioPERL, OrthoMCL, JAVA, ClustalW | http://www.grl.shizuoka.ac.jp/~thoriike/Ortholog-Finder | 2016 |
| Orthograph | Developed for a large data set maintaining the high sensitivity and accuracy with BRH approachs | Linux/Mac OS X | BLAST +, PERL, MySQL, MAFF, SWIPE | https://mptrsen.github.io/Orthograph/ | 2017 |
| Orthonome | Designed to boost the accuracy of multiple-species in ortholog predictions and reduce the trade-off between ortholog captures rates | Web-Server | Linux Bash, C++, Perl and Python package | http://www.orthonome.com/ | 2017 |
| OrthoVenn | Makes relationships of orthologous clusters across multiple species using Venn Diagram | Web-server | BLAST and MCL algorithms | http://aegilops.wheat.ucdavis.edu/OrthoVenn/ | 2015 |
| PanOCT | Automates clusters of orthologs for pan-genomic analysis of bacterial strains and closely related species | Linux/Unix | BLAST+, PERL | https://sourceforge.net/projects/panoct/ | 2012 |
| PhosphOrtholog | Developed for mapping of orthologs by protein PTMs by cross-species | Web-Server | BLOSUM62, comma separated file format (.csv) input | http://www.phosphortholog.com/ | 2015 |
| PorthoDom | Developed to speed up the detection of orthologs protein using domain sequences | Cross-platform | C program, Python, pFam Database, HMMER | http://www.bornberglab.org/pages/porthoda | 2015 |
| PorthoMCL | Designed for find orthologs in a large number of genomes | Linux and Unix (OS X) | BLAST, PERL, Python, MCL | http://ehsun.me/go/porthomcl/ | 2017 |
| ProteinOrtho | Dealing with hundreds of bacterial species in set containing millions of proteins using low computer memory | Linux/Unix 64 bits | BLAST+, PERL, and Python | http://www.bioinf.uni-leipzig.de/Software/proteinortho/ | 2011 |
| ReMark | Identifies orthologs automatically by a parameter adjustment according to the user's interest | Cross-platform (Java) | Recursive and a Markov clustering (MCL) algorithms, Reciprocal BLAST Best Hits (RBBH), JAVA | http://dasan.sejong.ac.kr/~wikim/notice.html | 2011 |
| SPOCS | Ortholog prediction on graph method based to generate a table can provide a visualization of the relationships between the orthologs groups | Web-Server; Linux/Mac OS X | BLAST+, C++ libraries | http://cbb.pnnl.gov/portal/tools/spocs.html (web) http://cbb.pnnl.gov/portal/software/spocs.html (installer) | 2013 |