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README 2022-03-07 1.3 kB
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seq_aln_tree.pl 2022-03-07 6.0 kB
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DESCRIPTION
A PERL SCRIPT WHICH REQUIRES ORTHOMCL GROUP.TXT OUTPUT AND A FASTA FILE WITH SEQUENCES OF IDS MENTIONED IN THE GROUP.TXT. THE SCRIPT EXTRACTS SEQUENCES OF EACH CLUSTER, ALIGNS THEM, TRIMS THE ALIGNMENT AND GENERATES A PHYLOGENETIC TREE. 

THE SCRIPT GENERATES FOLDERS NAMES cluseq, clualn, clualnt, clutree TO STORE THE SEQUENCES, ALIGNMENTS, TRIMMED ALIGNMENTS AND TREES. IF THESE FOLDERS EXIST THEN THE SCRIPT WILL STOP EXECUTION HENCE PLEASE ENSURE FOLDERS FROM PREVIOUS RUN ARE SAVED AS BACKUP AND REMOVED.



THE SCRIPT REQUIRES THE FOLLOWING PROGRAMS TO BE PRE INSTALLED

faSomeRecords (http://hgdownload.cse.ucsc.edu/admin/exe/)

muscle (www.drive5.com/muscle/)

trimal (http://trimal.cgenomics.org/)

FastTree (http://www.microbesonline.org/fasttree/)



THE FOLLOWINNG VARIABLES MUST BE SET WITHIN THE SCRIPT 

$farecord = ""; PATH TO THE faSomeRecords BINARY

$muscle = ""; PATH TO THE muscle BINARY

$trimal = ""; PATH TO THE trimal BINARY

$fatree = ""; PATH TO THE FastTree BINARY



USAGE: 

perl seq_aln_tree.pl <orthomcl output> <fasta file> <number of threads> <keyword>

THE KEYWORD IS A TAG TO SEARCH EACH CLUSTER AND ONLY IF THE TAG IS PRESENT THE CLUSTER IS CONSIDERED FOR FURTHER ANALYSIS. IF THE KEYWORD IS SET AS "." THEN ALL CLSUTERS ARE CONSIDERED.
Source: README, updated 2022-03-07