FSTAT - Revision history

Raj at 10:01, 10 January 2010

2010-01-10T10:01:54Z

← Older revision		Revision as of 10:01, 10 January 2010
Line 73:		Line 73:
	ITC2		ITC2
	ITC 3		ITC 3
			</pre>
	<pre>

	=How to cite=		=How to cite=
	Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/fstat.html. Updated from Goudet (1995)		Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/fstat.html. Updated from Goudet (1995)

			[[Category:Bioinformatics]]

Raj: /* Input */

2010-01-10T09:59:55Z

Input

← Older revision		Revision as of 09:59, 10 January 2010
Line 25:		Line 25:
	* Samples need not to be ordered		* Samples need not to be ordered
	* nu needs to be equal to the largest code given to an allele (even if there are less than nu alleles)		* nu needs to be equal to the largest code given to an allele (even if there are less than nu alleles)
			* Example
			<pre>
			3 5 4 1
			loc-1
			loc-2
			loc-3
			loc-4
			loc-5
			1 44 43 43 33 44
			1 44 44 43 33 44
			1 44 44 43 43 44
			2 44 44 33 32 44
			2 44 33 44 43 44
			2 44 43 44 43 44
			3 44 44 44 43 44
			3 44 44 44 44 44
			3 44 44 43 21 44
			</pre>

			<pre>
			3 5 4 2
			loc-1
			loc-2
			loc-3
			loc-4
			loc-5
			1 0404 0403 0403 0303 0404
			1 0404 0404 0403 0303 0404
			1 0404 0404 0403 0403 0404
			2 0404 0404 0303 0302 0404
			2 0404 0303 0404 0403 0404
			2 0404 0403 0404 0403 0404
			3 0404 0404 0404 0403 0404
			3 0404 0404 0404 0404 0404
			3 0404 0404 0403 0201 0404
			</pre>

			* additional label file:
			text file containing names (labels) for the population samples:
			* extension: .LAB
			* Each line should contain the name (label) of one sample
			* samples should appear in the same order as in the .DAT file
			* labels can be any length but will be truncated to six characters in the output files
			example:
			<pre>
			ITC1
			ITC2
			ITC 3

			<pre>

			=How to cite=
			Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/fstat.html. Updated from Goudet (1995)

Raj: Created page with '=FSTAT= STAT estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators…'

2010-01-10T09:56:26Z

Created page with '=FSTAT= STAT estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators…'

New page

=FSTAT=
STAT estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomisation methods. Jackknife and Bootstrap confidence intervals are also provided. The windows version also estimates statistics developed for the stepwise mutation model (Rst and the like)
=DATA type=
* SSR
* Standard (multi-allelic markers)
=Input=
* named FILENAME.DAT
* total number of individuals in the data set needs to be less than 20’000
* first line: contains 4 numbers separated by any number of spaces:
** number of samples, np (‹=200)
** number of loci, nl (‹=100)
** highest number used to label an allele, nu (‹=999)
** a 1 if the code for alleles is a one digit number (1-9), a 2 if code for alleles is a 2 digit number (01-99) or a 3 if code for alleles is a 3 digit number (001-999)
* followed by nl lines:
** each containing the name of a locus, in the order they will appear in the rest of the file
** On line nl+2, a series of numbers as follow: 1 0102 0103 0101 0203 0 0303
*** first number: identifies the sample to which the individual belongs
*** second: the genotype of the individual at the first locus, coded with a 2 digits number for each allele
*** third: the genotype at the second locus, until locus nl is entered (in the example above, nl=6)
* Missing genotypes are encoded with 0 (0001 or 0100 are not a valid format, so both alleles at a locus have to be known, otherwise, the genotype is considered as missing)
* no empty lines are needed between samples
* number of spaces between genotypes can be anything
* Numbering of samples need not be sequential
* the number of samples np needs to be the same as the largest sample identifier
* Samples need not to be ordered
* nu needs to be equal to the largest code given to an allele (even if there are less than nu alleles)