A couple of tools I find indispensable for post orthomcl down-stream analysis.
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Oct 2, 2019 - Perl
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orthomcl
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Pangenome-Analysis.py is written for extraction of core, accessory and unique genomes (Gene families and proteins) along with filtration of single copy orthologues, creation of binary and count matrices as well as removal of duplicates.
bioinformatics annotation clustering biology gene-families bioinformatics-analysis proteome-clustering downstream-analysis orthomcl pangenome singletons plasmodium duplicates-removal gene-family binary-matrix accessory-genes coregenome pangenome-inference pangenome-pipeline count-matrix
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Feb 21, 2022 - Python
💻 A unified bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across model organisms. Combines multi-database ortholog search with Gene Ontology annotation extension. 🎓 PhD project, King's College London (2013-2019).
bioinformatics biogrid uniprot homologene geneontology orthomcl orthologs homology eggnog drosophila-melanogaster homo-sapiens kings-college-london danio-rerio caenorhabditis-elegans orthology-relationships inparanoid arabidopsis-thaliana saccharomyces-cerevisiae orthologous-genes schizosaccharomyces-pombe
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Mar 16, 2026 - PHP
Orthologs Databases — Archive of bioinformatics databases and PHP processing pipelines for cross-species ortholog analysis across 7 model organisms (2012-2016). Integrates data from 21 sources including HomoloGene, InParanoid, OrthoMCL, eggNOG, BioGRID, STRING, Gene Ontology, KEGG, and Reactome.
php string databases biogrid biomart homologene flybase geneontology orthomcl kegg-ortholog orthologs orthology homology eggnog mitocheck inparanoid eggnog-mapper pombase signalink
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Mar 15, 2026 - PHP
We are taking existing orthoMcl Software Written Perl and Translating it to Python
python perl bioinformatics-pipeline protein-sequences bioinfomatics genomic genomic-data-analysis orthomcl
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May 18, 2017 - Perl
Scripts for comparative genomic analysis at the genome architechture and gene content level
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Aug 8, 2018
💻 Archive of my bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across five model organisms using orthology databases (eggNOG, inParanoid, Homologene etc.). 🎓 Part of my PhD project, King's College London (2013-2019).
bioinformatics drosophila uniprot homologene kegg reactome orthomcl orthologs orthology homology eggnog drosophila-melanogaster homo-sapiens kings-college-london inparanoid arabidopsis-thaliana saccharomyces-cerevisiae orthologous-genes pombase schizosaccharomyces-pombe
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Mar 16, 2026 - Hack
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