SIMPLE SOLUTIONS

ADDUNALIGNEDINTERVALS(1) - man page online | user commands

Part of mauveAligner package.

Chapter
April 2015
MAUVEALIGNER(1)                           User Commands                           MAUVEALIGNER(1)

NAME addUnalignedIntervals - part of mauveAligner package alignmentProjector - part of mauveAligner package backbone_global_to_local - part of mauveAligner package bbAnalyze - part of mauveAligner package createBackboneMFA - part of mauveAligner package getAlignmentWindows - part of mauveAligner package getOrthologList - part of mauveAligner package makeBadgerMatrix - part of mauveAligner package mauveToXMFA - part of mauveAligner package mfa2xmfa - part of mauveAligner package projectAndStrip - part of mauveAligner package randomGeneSample - part of mauveAligner package scoreAlignment - part of mauveAligner package stripGapColumns - part of mauveAligner package stripSubsetLCBs - part of mauveAligner package toGrimmFormat - part of mauveAligner package toMultiFastA - part of mauveAligner package toRawSequence - part of mauveAligner package uniqueMerCount - part of mauveAligner package uniquifyTrees - part of mauveAligner package xmfa2maf - part of mauveAligner package
DESCRIPTION These tools belong to the mauveAligner package. They are not explicitly documented but are printing a synopsis line which is repeated here. addUnalignedIntervals <input interval file> <output interval file> alignmentProjector <input xmfa> <output xmfa> <mfa seq input> <mfa seq output> <list of seqs to include, starting at 0> backbone_global_to_local <xmfa file> <backbone file> <output file> bbAnalyze <xmfa file> <guide tree> <backbone seqpos file> <backbone col file> <annotated seq index> <output file> annotated seq index starts at 0. createBackboneMFA <input interval file> <output MFA name> getAlignmentWindows <XMFA alignment> <window length> <window shift amount> <base output filename> getOrthologList getOrthologList <input xmfa> <backbone seq file> <reference genome> <CDS ortholog filename> <CDS alignment base name> makeBadgerMatrix makeBadgerMatrix <input xmfa> <output badger file> <LCB coordinate file> mauveToXMFA mauveToXMFA <Mauve Alignment input> <XMFA output> mfa2xmfa <MFA alignment input> <XMFA alignment output> [Unaligned FastA output] projectAndStrip <input xmfa> <output xmfa> <seq1> <seq2>...<seqN> Numeric sequence identifiers start at 0. randomGeneSample <input xmfa> <backbone seq file> <sample genome> <number of genes> <out‐ put base name> [random seed] scoreAlignment <correct alignment> <calculated alignment> [evolved sequence file] [slagan] stripGapColumns <input XMFA> <output XMFA> stripSubsetLCBs <input xmfa> <input bbcols> <output xmfa> [min LCB size] [min genomes] [randomly subsample to X kb] toGrimmFormat <Mauve Alignment> <genome 1 chr lengths>...<genome N chr lengths> toMultiFastA <input interval file> <output base name> toRawSequence <input sequence> <output file> uniqueMerCount <Sorted Mer List> uniquifyTrees <nexus input file> <nexus output file> All trees in the input file must have the same number of taxa and the same taxon labels xmfa2maf <xmfa input> <maf output>
mauvealigner 1.2.0+4713 April 2015 MAUVEALIGNER(1)
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addUnalignedIntervals(1) referred by
refer to mauveAligner(1)