fafind-eq-seq - find equal sequences


    ./fafind-eq-seq [--help] [--eval 'perlcode'] <file1> [<file2> ... <fileN>] >file_with_results.txt

    ./fafind-eq-seq [--help] [--eval 'perlcode'] --filter <file1> [<file2> ... <fileN>] >file_with_only_unique_seqs.fasta


Find identical / equal sequences in a given set of fasta files. Info messages go to standard error (stderr), results to standard output (stdout).

The result output of file_with_results.txt consists of lines following the pattern


whereas each unindented line and the following <TAB>-indented lines mark one group of identical sequences.



Do not print the groups but the sequences in fasta format instead. Duplicated sequences are omitted. The resulting fasta output is not checked for identical ids, etc.

Synonyms: -f


Display this message.

Synonyms: -?, -h


Manipulate input sequences on the fly. The current sequence string is set to $_.

This doesn't change the actual output sequence, e.g. on filtering.

Can be very handy for comparing aa-sequences from two different files, at which one file uses * as stop codon and the other file not:

    ./fafind-eq-seq --eval 's/\*$//' <file1> <file2> >file_with_results.txt

Synonyms: -e


jw bargsten, <joachim.bargsten at>