Mugsy 1.2.1

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.<br />Installation<br /><br /> * Download mugsy from Sourceforge<br /><br /> cd /path/to/install<br /> tar xvzf mugsy_x86-64-vNrN.tgz<br /><br /> Mugsy sources are compiled for x86-64-bit architectures and invoked from a Perl wrapper script.<br /><br /> * Edit mugsyenv.sh and add path to the installation area<br /><br /> export MUGSY_INSTALL=/path/to/install/mugsy<br /><br /><br /> mugsyenv.sh can then be sourced before invoking mugsy. Alternatively, you can add MUGSY_INSTALL to your environment. <br /><br />Getting started<br /><br /> * Set up the environment<br /><br /> bash<br /> source /path/to/install/mugsyenv.sh<br /><br /><br /> * Run mugsy<br /> The input to Mugsy is DNA from two or more genomes in FASTA format. The genomes must be assembled into contigs or scaffolds. For draft genomes, a single multi-FASTA file containing all contigs for the genome should be provided.<br /><br /> mugsy --directory /data/output --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta <br /><br /><br />This example will align three genomes and output a file /data/output/mygenomes.maf. The --directory setting is also used for storing temporary files during the run.<br /><br />The prefix of each input filename will be used as the genome name in the output files (eg. genome1 from genome1.fsa). Header lines in the FASTA files should not contain ':' or '-' to avoid parsing problems.<br /><br /># View or parse MAF output<br />The output of Mugsy is Multiple Alignment Format (MAF). GMAJ is a reference-based stand-alone viewer for MAF files.

Requirements:	No special requirements
Platforms:	Mac, Mac OSX
Keyword:	Alignment,  Contigs,  Directory,  Draft,  Environment,  Fasta,  Files,  Genome,  Genomes,  Input,  Mugsy,  Mugsyenvsh,  Multifasta,  Multiple,  Output,  Prefix
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