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Home modified by Pasi Rastas

Pasi Rastas — Mon, 14 Mar 2016 17:52:45 -0000

--- v36
+++ v37
@@ -3,7 +3,7 @@

 Pasi Rastas, (C) 2015-2016, pasi.rastas@gmail.com

-Lep-MAP2 (LM2) is a novel linkage map construction suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them. 
+Lep-MAP2 (LM2) is a novel linkage map construction software suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them. 

 The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download [here](https://sourceforge.net/projects/lepmap2/files/sim.zip). Also some useful scripts can be downloaded [here](https://sourceforge.net/projects/lepmap2/files/scripts.zip).

Home modified by Pasi Rastas

Pasi Rastas — Fri, 05 Feb 2016 16:23:41 -0000

--- v35
+++ v36
@@ -1,7 +1,7 @@
 Lep-MAP2 : Documentation
 ====

-Pasi Rastas, (C) 2015, pasi.rastas@gmail.com
+Pasi Rastas, (C) 2015-2016, pasi.rastas@gmail.com

 Lep-MAP2 (LM2) is a novel linkage map construction suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them.

Home modified by Pasi Rastas

Pasi Rastas — Wed, 13 Jan 2016 09:30:47 -0000

--- v34
+++ v35
@@ -26,4 +26,4 @@

 vcf2posterior.awk : this will convert vcf files to Lep-MAP posteriors (takes PL field from a vcf). The pedigree information must be added separately.

-Note: script transpose_tab can become very slow with many markers. Now there is the Transpose module in Lep-MAP that does transposes faster (replace "./transpose_tab" with "java [-cp bin] Tranpose").
+Note: script transpose_tab can become very slow with many markers. Now there is the Transpose module in Lep-MAP that does transposes faster (replace "./transpose_tab" with "java \[-cp bin\] Tranpose").

Home modified by Pasi Rastas

Pasi Rastas — Wed, 13 Jan 2016 09:30:15 -0000

--- v33
+++ v34
@@ -25,3 +25,5 @@
 loc2linkage : this will convert JoinMap files to linkage files

 vcf2posterior.awk : this will convert vcf files to Lep-MAP posteriors (takes PL field from a vcf). The pedigree information must be added separately.
+
+Note: script transpose_tab can become very slow with many markers. Now there is the Transpose module in Lep-MAP that does transposes faster (replace "./transpose_tab" with "java [-cp bin] Tranpose").

Home modified by Pasi Rastas

Pasi Rastas — Wed, 28 Oct 2015 01:00:26 -0000

--- v32
+++ v33
@@ -23,3 +23,5 @@
 linkage2post.awk, simpleconvert.awk : these are used to convert linkage files to posteriors and back, needed to run ParentCall (to impute missing parental genotypes or to call markers in the sex chromosome)

 loc2linkage : this will convert JoinMap files to linkage files
+
+vcf2posterior.awk : this will convert vcf files to Lep-MAP posteriors (takes PL field from a vcf). The pedigree information must be added separately.

Home modified by Pasi Rastas

Pasi Rastas — Thu, 04 Jun 2015 13:20:38 -0000

--- v31
+++ v32
@@ -5,7 +5,7 @@

 Lep-MAP2 (LM2) is a novel linkage map construction suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them. 

-The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download [here](https://sourceforge.net/projects/lepmap2/files/sim.zip). Also some useful scripts can be downloaded [here](https://sourceforge.net/projects/lepmap2/files/scipts.zip).
+The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download [here](https://sourceforge.net/projects/lepmap2/files/sim.zip). Also some useful scripts can be downloaded [here](https://sourceforge.net/projects/lepmap2/files/scripts.zip).

 Installation
 ----

Home modified by Pasi Rastas

Pasi Rastas — Thu, 04 Jun 2015 13:20:10 -0000

--- v30
+++ v31
@@ -5,7 +5,7 @@

 Lep-MAP2 (LM2) is a novel linkage map construction suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them. 

-The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download [here](https://sourceforge.net/projects/lepmap2/files/sim.zip). Also some useful scripts can be downloaded [here](https://sourceforge.net/projects/lepmap2/files/sim.zip).
+The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download [here](https://sourceforge.net/projects/lepmap2/files/sim.zip). Also some useful scripts can be downloaded [here](https://sourceforge.net/projects/lepmap2/files/scipts.zip).

 Installation
 ----

Home modified by Pasi Rastas

Pasi Rastas — Thu, 04 Jun 2015 13:19:33 -0000

--- v29
+++ v30
@@ -5,7 +5,7 @@

 Lep-MAP2 (LM2) is a novel linkage map construction suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them. 

-The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download here. Also some useful scripts can be downloaded here.
+The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download [here](https://sourceforge.net/projects/lepmap2/files/sim.zip). Also some useful scripts can be downloaded [here](https://sourceforge.net/projects/lepmap2/files/sim.zip).

 Installation
 ----

Home modified by Pasi Rastas

Pasi Rastas — Thu, 04 Jun 2015 13:17:00 -0000

--- v28
+++ v29
@@ -3,7 +3,7 @@

 Pasi Rastas, (C) 2015, pasi.rastas@gmail.com

-Lep-MAP2 (LM2) is a novel linkage map construction suite. I can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them. 
+Lep-MAP2 (LM2) is a novel linkage map construction suite. It can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them. 

 The following wiki will document its features. Each module of LM2 is documented in [Modules] with examples on simulated data. The used data can download here. Also some useful scripts can be downloaded here.

Home modified by Pasi Rastas

Pasi Rastas — Thu, 14 May 2015 09:38:09 -0000

--- v27
+++ v28
@@ -1,7 +1,7 @@
 Lep-MAP2 : Documentation
 ====

-Pasi Rastas, pasi.rastas@gmail.com
+Pasi Rastas, (C) 2015, pasi.rastas@gmail.com

 Lep-MAP2 (LM2) is a novel linkage map construction suite. I can handle tens of thousands of markers and individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them.