SNAP Map
SNAP Map is a command line-based tool that collapses DNA sequence data into unique haplotypes, extracts variable sites, and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map includes novel features such as recoding indels, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype-phenotype associations. SNAP Map was designed and tested on Mac OS X 10.3/10.4, Windows 2000/XP, and Red Hat Enterprise Desktop Linux, Version 2.4 distribution.
TO INSTALL:
Download the file archive for your platform and extract the contents.
COMMAND LINE
map [options] [INFILE...] [-oX OUTFILE...]
EXAMPLE
map -cvgm CHV1.phy -i2 CHV1_locality -o1 CHV1.out -o2 CHV1.hapkey -o3 CHV1.map -o4 CHV1.genetree -o5 CHV1.ancestor
OPTIONS
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-s |
Include only variable sites |
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-c |
Collapse individuals into unique haplotypes |
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-G |
Remove columns that are part of a indel |
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-g |
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-v |
Remove columns with Infinite Sites Model violations |
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-m |
Remove columns with missing data |
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-b |
Represent variable sites as 1 and 0 only |
INPUT FORMATS
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-i2 |
This is an optional input file containing phenotype information by individual. This affects -o1, -o4, and -o9 outputs. |
OUTPUT FORMATS
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Output Option |
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Application or Description |
Reference |
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-o1 |
No |
PHYLIP |
Felsenstein, 2004 |
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Yes |
MDIV1 |
Nielson and Wakeley, 2001 |
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-o2 |
No |
Lists individuals by haplotype |
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-o3 |
No |
Our MAP output illustrates data features such as variable sites, consensus sequence, and frequency of haplotypes. |
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-o4 |
Optional |
GENETREE |
Griffiths and Tavaré, 1994 |
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-o5 |
Optional |
GENETREE ancestor file is essentially the first row of the genetree output. |
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-o6 |
No |
RECMIN |
Myers and Griffiths, 2003 |
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-o7 |
No |
RECPARS |
Hein, 1993 |
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-o8 |
No |
RECOM58 |
Griffiths and Marjoram, 1996 |
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-o9 |
Yes |
HUDSON2 |
Hudson, 2000; Hudson, et al., 1992 |
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-o0 |
Yes |
MIGRATE3 |
Beerli, 2006; Beerli and Felsenstein, 1999 |
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-oA |
No |
Neutrality tests |
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-oB |
No |
Lists the position of all variable sites in multiple alignment. |
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-oC |
No |
SHRUB and HAPBOUND |
Song et al., 2005 |
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No |
BEAGLE |
Lyngsø et al., 2005 |
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1IM ( Hey and Nielsen, 2004 ) is also supported.
2Refers to the programs Seqtomatrix and Permtest developed by R. Hudson.
3Can also combine multiple single locus MIGRATE files into one multilocus file using MLCombine in Combine distribution.
