📦 murasaki-common

A

• align2kog.pl(1)converts an alignment into a kog file✨
• analyze-pat.pl(1)analyzes a pattern✨

C

• chromostitch.pl(1)Makes stitch files for feeding to geneparse.pl to allow feeding of multiple chromosomes to programs like murasaki✨

F

• faformat.pl(1)Reformat a sequence into fasta format✨
• filter.pl(1)filters output from murasaki based on various filters✨

G

• 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✨

H

• histocomp.pl(1)plot multiple histograms on one graph✨
• histoplot.pl(1)plots histograms✨
• homology-score.pl(1)generates homology scorse from murasaki anchor files✨

I

• interpolate.pl(1)chop anchors into arbitrarily sized tiny anchor bits, interpolate anchor break points based on individual anchor lengths.✨

K

• kogalign.pl(1)produce (untested) alignments from cds files✨

L

• lav2murasaki.pl(1)convert a LAV file (ie: from Blastz) into a Murasaki set of files✨

M

• 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 anchor format based on gapped alignment data (each gap triggers a new anchor). Note this refers to the Mauve alignment format, not the LAGAN .alignment file…✨
• mbgd-to-kog.pl(1)converts mbgd cluster files to kog files✨
• mfasplit.pl(1)splits mfa (MultiFASTA) files into individual fa files✨

N

• names2kog.pl(1)builds a kog-set based only on gene "names"✨

O

• overlay.pl(1)overlay a couple of images, offsetting the hue in each✨

P

• phAlignment2anchors.pl(1)converts a PatternHunter alignment into Murasaki anchor format✨

Q

• qlob.pl(1)run quick mursaki compare✨

R

• 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)computes ROC/sensitivity/specificity at various/all thresholds✨

S

• simpal.pl(1)proof of concept✨
• simplegraph.pl(1)Provides dotplot/chaos style plot of murasaki alignments✨
• stat-histo.pl(1)density plot of some given stat✨
• stat-vs-stat.pl(1)draws graphs of 1 stat vs another stat✨
• substitch.pl(1)Split/merge stitch files into/out of stitch files✨