pseqsid

Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.

Usage

USAGE:
    pseqsid [OPTIONS] <MSA>

ARGS:
    <MSA>    Multiple Sequence Alignment file

OPTIONS:
    -i, --identity               Calculate pairwise sequence identity
    -s, --similarity             Calculate pairwise sequence similarity
    -n, --nss                    Calculate pairwise sequence Normalized Similarity Score
    -l, --length <LENGTH>        Sequence length to be use for identity and similarity calculations
                                 [default: smallest] [possible values: smallest, mean, largest,
                                 alignment]
    -g, --grouping <GROUPING>    Similarity amino acid grouping definition file. A default one is
                                 created if required and not provided
    -m, --matrix <MATRIX>        Type of matrix to be used for Normalized Similarity Score [default:
                                 blosum62] [possible values: blosum62, pam250, gonnet]
    -t, --threads <THREADS>      Number of threads to use. 0 use all available threads [default: 0]
    -h, --help                   Print help information
    -V, --version                Print version information

At least one option from -i, -s, and/or -n must be supplied for the program to do something.

Notes

At this moment just the identity calculation is implemented More information will be supplied when the implementation of all features progress.

Installation

cargo install pseqsid

Or you can download and build the crate yourself.

Examples

pseqsid -i msa_protein.fasta