- Install sml in terminal mac mac os x#
- Install sml in terminal mac software#
- Install sml in terminal mac windows#
island-output= Output islands the given file (requires –island-size) island-size= Find islands larger than the given number id-matrix= Generate LCB stats and write them to the specified file Should be given two or more times to with different paths. scratch-path= For large genomes, use a directory for storage of temporary data. lcb-input= Use specified lcb file instead of constructing LCBs (skips LCB generation) lcb-match-input Indicates that the match input file contains matches that have been clustered into LCBs match-input= Use specified match file instead of searching for matches weight= Minimum LCB weight in base pairs per sequence eliminate-inclusions Eliminate linked inclusions in subset matches. max-extension-iterations= Limit LCB extensions to this number of attempts, default is 4 seed-size= Initial seed match size, default is log2( average seq. no-lcb-extension If determining LCBs, don’t attempt to extend the LCBs no-recursion Don’t perform recursive anchor identification (implies –no-gapped-alignment) mums Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) Many other command line options can be given to the mauveAligner binary. MauveAligner -weight=300 -output=two_yeast.mauve -output-alignment=two_yeast.alignment S_cerevisiae.gbk S_ S_bayanus.gbk S_ Aligning two yeast genomes, increasing the weight threshold to avoid spurious LCBs: MauveAligner -collinear -output=hcv.mauve -output-alignment=hcv.alignment hcv.mfaĮxample 5. Aligning a group of Hepatitis C virii known to have no rearrangements: MauveAligner -no-recursion -no-gapped-alignment -o poxvirus.mauve all_poxvirus.mfaĮxample 4. Generating initial alignment anchors without actually aligning: MauveAligner -output=poxvirus.mauve -output-alignment=poxvirus.alignment all_poxvirus.mfaĮxample 3. Aligning several poxvirus genomes stored in a single Multi-FastA file: MauveAligner -output=ec_sa.mauve -output-alignment=ec_vs_sa.alignment ecoli.gbk salmonella.gbk Įxample 2. coli and Salmonella genomes stored in separate GenBank files: In this case mauveAligner assumes one genome per Multi-FastA sequence entry and will align the entries to each other.Įxample 1. Alternatively, mauveAligner can be given the name of a Multi-FastA file containing all the genomes to align. If the SML file does not exist, mauveAligner will create it. If an individual file contains several sequence entries, they will be concatenated and the whole concatenated sequence will be aligned to the sequences in the other files.Įach sequence must have a corresponding Sorted Mer List (SML) file name given. Sequence files can be in FastA, Multi-FastA, or GenBank flat file format.
mauveAligner arguments and examplesĮach entry like denotes the name of a sequence file on disk that contains a genome to align. See the Mauve Developer’s Guide for more details.
Install sml in terminal mac software#
On Linux the mauveAligner and progressiveMauve binaries are in the top level directory of the software distribution, with 64-bit binaries in the linux-圆4 subdirectory.Īlternatively, mauveAligner and progressiveMauve can be compiled from source for your particular platform. However, if using Mauve versions 2.0.0 or earlier, be sure to also copy the muscle_aed binary to the same location. The binaries can be copied to a more convenient location. Relative to Mauve.app the paths will be Mauve.app/Contents/MacOS/mauveAligner and Mauve.app/Contents/MacOS/progressiveMauve.
Install sml in terminal mac mac os x#
On Mac OS X the mauveAligner and progressiveMauve binaries are packaged within the Mauve application.
Install sml in terminal mac windows#
On 64-bit Windows platforms, the binaries in the win64 subdirectory may be used instead. On Windows they are located in the directory where Mauve was installed, usually C:\Program Files\Mauve\. MauveAligner and progressiveMauve are included with the Mauve software. Where to find mauveAligner and progressiveMauve When run from the command-line, these programs provide options not yet available in the graphical interface. The mauveAligner and progressiveMauve alignment algorithms have been implemented as command-line programs included with the downloadable Mauve software.
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