Murasaki-Common
- align2kog.pl(1) converts an alignment into a kog file
- analyze-pat.pl(1) pat.pl -- analyzes a pattern
- chromostitch.pl(1) Makes stitch files for feeding to geneparse.pl to allow feeding of multiple chromosomes to programs like murasaki
- faformat.pl(1) - Reformat a sequence into fasta format
- filter.pl(1) filters output from murasaki based on various filters
- gatherstats.pl(1) - gathers stats from all sorts of sources
- getcds.pl(1) CDS extraction from various annotation formats
- getgene.pl(1) grab the dna for a gene using annotation
- histocomp.pl(1) - plot multiple histograms on one graph
- histoplot.pl(1) - plots histograms
- homology-score.pl(1) score.pl - generates homology scorse from murasaki anchor files
- interpolate.pl(1) chop anchors into arbitrarily sized tiny anchor bits,
- kogalign.pl(1) - produce (untested) alignments from cds files
- lav2murasaki.pl(1) - convert a LAV file (ie: from Blastz) into a Murasaki set of files
- maf2anchors.pl(1) - Converts maf files into Murasaki anchor sets
- mauve2anchors.pl(1) converts a Mauve alignment into Murasaki anchor format
- mauveAlignment2anchors.pl(1) converts a Mauve alignment into Murasaki
- mbgd-to-kog.pl(1) to-kog.pl - converts mbgd cluster files to kog files
- mfasplit.pl(1) - splits mfa (MultiFASTA) files into individual fa files
- names2kog.pl(1) builds a kog-set based only on gene "names"
- overlay.pl(1) overlay a couple of images, offsetting the hue in each
- phAlignment2anchors.pl(1) converts a PatternHunter alignment into Murasaki anchor format
- qlob.pl(1) - run quick mursaki compare
- rearrange.pl(1) - rearrange an anchors file according to some rules
- repeats2anchors.pl(1) - generates a phony alignment (suitable for graphing) out of a .repeats file
- repeatviz.pl(1) - visualize a bunch of repeats using graphviz
- roc-at-cutoff.pl(1) at-cutoff.pl - computes ROC/sensitivity/specificity at various/all
- simpal.pl(1) - proof of concept
- simplegraph.pl(1) Provides dotplot/chaos style plot of murasaki alignments
- stat-histo.pl(1) histo.pl -- density plot of some given stat
- stat-vs-stat.pl(1) vs-stat.pl -- draws graphs of 1 stat vs another stat
- substitch.pl(1) - Split/merge stitch files into/out of stitch files