MAUVEALIGNER(1)

🦋 MAUVEALIGNER(1) · User Commands 🦋

okay so this is the MAUVEALIGNER(1) page, the user commands manual for the mauveAligner package 🎀 bestie, it's giving main character energy 💖

✨ NAME ✨

Here's the whole squad 🧚 every single one is part of the mauveAligner package:

• addUnalignedIntervals — part of the mauveAligner package 🌸
• alignmentProjector — part of the mauveAligner package 🌸
• backbone_global_to_local — part of the mauveAligner package 🌸
• bbAnalyze — part of the mauveAligner package 🌸
• createBackboneMFA — part of the mauveAligner package 🌸
• getAlignmentWindows — part of the mauveAligner package 🌸
• getOrthologList — part of the mauveAligner package 🌸
• makeBadgerMatrix — part of the mauveAligner package 🌸
• mauveToXMFA — part of the mauveAligner package 🌸
• mfa2xmfa — part of the mauveAligner package 🌸
• projectAndStrip — part of the mauveAligner package 🌸
• randomGeneSample — part of the mauveAligner package 🌸
• scoreAlignment — part of the mauveAligner package 🌸
• stripGapColumns — part of the mauveAligner package 🌸
• stripSubsetLCBs — part of the mauveAligner package 🌸
• toGrimmFormat — part of the mauveAligner package 🌸
• toMultiFastA — part of the mauveAligner package 🌸
• toRawSequence — part of the mauveAligner package 🌸
• uniqueMerCount — part of the mauveAligner package 🌸
• uniquifyTrees — part of the mauveAligner package 🌸
• xmfa2maf — part of the mauveAligner package 🌸

💅 DESCRIPTION 💅

okay so these tools all live in the mauveAligner package 🧚 lowkey, they aren't explicitly documented 🙈 but each one prints a synopsis line when you run it, so we're repeating those here so you never have to guess 💀 iykyk

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>

⚠️ bestie, listen: all trees in the input file must have the same number of taxa and the same taxon labels, or uniquifyTrees is not going to be happy 😭

xmfa2maf <xmfa input> <maf output>

Okay bestie, that's the whole tea ☕ this page is mauvealigner 1.2.0+4713 from April 2015, so go forth and align responsibly 🫶🌈💅