Alignment Statistics

The format of the input file is basically aligned fasta.

There is an example format file, alignment_stats.txt. First run this program on that file to see what it does. You can click here to run it directly.

The requirements are as follows:
A) All aligned residues are upper case -->lower case residues are considered unaligned
B) The lengths of sequences are all the same
C) The fasta identifiers are at least 4 characters long. The first four characters are used for the output A blank line separating sequence blocks of aligned fasta sequences causes the output for each sequence_block to be reported separately aswell as the total for the whole file.

You may optionally specify the regions of the alignment to report. The numbers should be given in a space or comma separated list of hyphenated or spaced pairs. The numbers refer to the ungapped position in the first (master) sequence. Eg. 3-15,20-29,30-41,50-97