Man pages for iferres/phylen
Search Core Genes Using HMMs, Compute Multiple Alignment, Concatenate And Compute Phylogeny
| catHoriz | Concatenate The Coregenes |
| catVert | Concatenate All Supergenes In A Single Fasta File |
| comp | Complements a nucleic acid sequence |
| computePhylo | Compute Phylogeny |
| download_nog_hmm | Download specific hmm datasets from EggNOG. |
| extractGffTable | Extract the gff3 table and make it 'R'eadable. |
| extractSeqsFromGff3 | Extract Sequences from Gff3 file |
| getFfnFaa | Extract CDS gene (DNA) and protein (AA) sequences |
| getIdsFromStats | Get Pfam Ids From Hmmstats output |
| hmmPress | hmmPress |
| hmmSearch | Run hmmsearch (HMMER 3) |
| hmmStat | Compute Hmm Stats |
| list_eggnogdb | List available EggNOG db datasets |
| mafft | Align with MAFFT aligner |
| phylen | Compute Core Genome Alignment And Phylogeny |
| readDomtblout | Process hmmsearch output to make it 'R'eadable. |
| setHMM | Prepare Compressed Hmm Files To Hmmsearch |
| translate | Translate |
| untargz | Decompress A Tar.gz File |
