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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.

TO INSTALL:

Download the file archive for your platform and extract the contents.

map_mac.zip

map_windows.zip

map_linux.zip

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.

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

-s

Include only variable sites

-c

Collapse individuals into unique haplotypes

-G

Remove columns that are part of a indel

-g

Recode indels such that each allele has a unique number

-v

Remove columns with Infinite Sites Model violations

-m

Remove columns with missing data

-b

Represent variable sites as 1 and 0 only

INPUT FORMATS

-i2

This is an optional input file containing phenotype information by individual. This affects -o1, -o4, and -o9 outputs.

OUTPUT FORMATS

Output Option	Includes Phenotypic Information	Application or Description	Reference
-o1	No	PHYLIP	Felsenstein, 2004
-o1	Yes	MDIV¹	Nielson and Wakeley, 2001
-o2	No	Lists individuals by haplotype
-o3	No	Our MAP output illustrates data features such as variable sites, consensus sequence, and frequency of haplotypes.
-o4	Optional	GENETREE	Griffiths and Tavaré, 1994
-o5	Optional	GENETREE ancestor file is essentially the first row of the genetree output.
-o6	No	RECMIN	Myers and Griffiths, 2003
-o7	No	RECPARS	Hein, 1993
-o8	No	RECOM58	Griffiths and Marjoram, 1996
-o9	Yes	HUDSON²	Hudson, 2000; Hudson, et al., 1992
-o0	Yes	MIGRATE³	Beerli, 2006; Beerli and Felsenstein, 1999
-oA	No	Neutrality tests
-oB	No	Lists the position of all variable sites in multiple alignment.
-oC	No	SHRUB and HAPBOUND	Song et al., 2005
-oC	No	BEAGLE	Lyngsø et al., 2005

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.

TO INSTALL:

Download the file archive for your platform and extract the contents.

map_mac.zip

map_windows.zip

map_linux.zip

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.

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

-s

Include only variable sites

-c

Collapse individuals into unique haplotypes

-G

Remove columns that are part of a indel

-g

Recode indels such that each allele has a unique number

-v

Remove columns with Infinite Sites Model violations

-m

Remove columns with missing data

-b

Represent variable sites as 1 and 0 only

INPUT FORMATS

-i2

This is an optional input file containing phenotype information by individual. This affects -o1, -o4, and -o9 outputs.

OUTPUT FORMATS

Output Option

Includes Phenotypic Information

Application or Description

Reference

-o1

No

PHYLIP

Felsenstein, 2004

Yes

MDIV1

Nielson and Wakeley, 2001

-o2

No

Lists individuals by haplotype

-o3

No

Our MAP output illustrates data features such as variable sites, consensus sequence, and frequency of haplotypes.

-o4

Optional

GENETREE

Griffiths and Tavaré, 1994

-o5

Optional

GENETREE ancestor file is essentially the first row of the genetree output.

-o6

No

RECMIN

Myers and Griffiths, 2003

-o7

No

RECPARS

Hein, 1993

-o8

No

RECOM58

Griffiths and Marjoram, 1996

-o9

Yes

HUDSON2

Hudson, 2000; Hudson, et al., 1992

-o0

Yes

MIGRATE3

Beerli, 2006; Beerli and Felsenstein, 1999

-oA

No

Neutrality tests

-oB

No

Lists the position of all variable sites in multiple alignment.

-oC

MDIV¹

HUDSON²

MIGRATE³

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.