SeqRuler

A simple GUI interface for calculating TN93 distance or SNP (Hamming) distance between all sequences in an input fasta file.

Download

• Download: SeqRuler.jar

Or compile from source

• Compilation: bash mvn clean install

Running

bash java -jar SeqRuler.jar

Help

bash Usage: java -jar SeqRuler.jar [-egGhnprsSV] [-a=<ambiguityHandling>] [-c=<cores>] [-d=<distanceMethod>] [-f=<max_ambiguity_fraction>] [-i=FILE] [-o=FILE] [-t=<edgeThresholdString>] -a, --ambiguity, --ambiguities=<ambiguityHandling> How to handle ambiguous nucleotides. One of [resolve, average, gapmm, skip] -c, --cores=<cores> Number of cores to use for parallel processing. Default: 1 -d, --distance-method=<distanceMethod> distance metric to use. One of [TN93, SNP]. Default: TN93 -e, --enumerate_sequences Enumerate sequences for output file, and produce additional map file giving integer to sequence name mapping. Default: false -f, --fraction=<max_ambiguity_fraction> Maximum allowable fraction of ambiguities allowed for 'resolve' mode. If exceeded, uses 'average' mode. -g, --ignore-terminal-gaps Ignore terminal gaps at beginning and end of sequences when calculating distances. [SNP only] Default: true -G, --ignore-all-gaps Ignore all gaps when calculating distances. [SNP only] Default: false -h, --help Show this help message and exit. -i, --inFile=FILE input file with sequences -n, --ignore-ambiguities Ignore ambiguities when calculating distances. [SNP only] Default: true -o, --outFile=FILE output file with distances -p, --pairs read pairs of sequences from stdin, calculate distance for each pair. format "name1, seq1, name2, seq2\n". Do not include a header row -r, --run-server run jetty server -s, --stdin read fasta from stdin. Alternative to reading from a file (-i) -S, --stdout write distances to stdout. Alternative to writing to a file (-o) -t, --edge-threshold=<edgeThresholdString> edges above the threshold are not reported in output. {Default: 1.0 (TN93), inf (SNP)} -V, --version Print version information and exit.