SUPERFAMILY 1.75 HMM library and genome assignments server

Calculate Alignment Statistics for Aligned Fasta Sequences

Calculate alignment statistics for your aligned fasta sequences.

The format of the input file is basically aligned fasta. There is an example file, alignment_stats.txt.
Calculate alignment statistics for the example file.

The alignment 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

Normalise, weighting each block equally?