svr_insert_seqs_into_alignment

    svr_insert_seqs_into_alignment [options] Seqs < old_ali.fa > new_ali.fa

This script takes a FASTA file of protein/DNA alignment from the standard input and the name of a FASTA file of sequences to be inserted from the command line and writes the resulting alignment to the standard output. When not possible, a message will be written to the standard error output.

Seqs is the name of the FASTA file that contains the sequences to be inserted.

Command-Line Options

trim

Trim sequence start and end.

verbose

Print information messages to the standard error output.

stddev

Window of similarity to include in profile (D = 1.5).

Output Format

The standard output is a FASTA file which contains the inserted sequences.