---
name: "addUnalignedIntervals"
section: "1"
platform: "linux"
package: "progressivemauve"
version: "1.2.0+4713+dfsg-5+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/addUnalignedIntervals"
---

# addUnalignedIntervals(1)

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

## 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\> \<output 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\>*