OrthomclFilterFasta creates goodProteins.fasta (or goodNucleotides.fasta) file containing all good proteins or DNA and rejectProteins.fasta (rejectNucleotides.fasta) containing all rejects. Input is a directory containing a set of compliant input .fasta files (as produced by orthomclAdjustFasta).
Parent program: orthomcl
OrthoMCL allows automatic identification of orthologous groups. The OrthoMCL uses NCBI reciprocal (one-to-one) BLAST and Markov clustering algorithms in conjunction with a relational database (MySQL) to store the intermediate data. OrthoMCL produces results similar to INPARANOID when applied to two genomes. OrthoMCL differs from the EGO strategy and the COG algorithm commonly applied to prokaryotic genomes and allows an improved recognition of 'recent' paralogs.