File	Date	Author	Commit
scripts	2025-03-05	Rastas Pasi M A	[7e641a] OrderMarkers2 speed and memory optimisations, s...
src	2025-03-12	Rastas Pasi M A	[e5dd07] greedyPhaser
COPYING	2016-09-19	pmr47	[0b8bea] Bugfixes
README	2022-06-17	Pasi Rastas	[baa04f] CallMutations
qtl.R	2021-05-04	Pasi Rastas	[ab4833] QTL pipeline
qtl.png	2021-05-04	Pasi Rastas	[ab4833] QTL pipeline
qtlPerm.R	2021-05-04	Pasi Rastas	[ab4833] QTL pipeline
qtldata1.12	2021-05-04	Pasi Rastas	[ab4833] QTL pipeline
qtlphenotypes.txt	2021-05-04	Pasi Rastas	[ab4833] QTL pipeline

Read Me

Lep-MAP3 (v. 0.5)

Linkage map construction suite

See Lep-MAP3 wiki on sourceforge for documentation.

The files included:

simulated_data.zip    : Used simulated data, commands to run and evaluate MSTmap and Lep-MAP3 on the data
simulated_scripts.zip : Only the scripts to generate the simulated data
binary+code.zip       : Lep-MAP3 binaries + source code
binary.zip            : Lep-MAP3 binaries only

How to run Lep-MAP3 (compiled classes located in the folder bin):

java -cp bin/ ParentCall2
java -cp bin/ Filtering2
java -cp bin/ SeparateChromosomes2
java -cp bin/ JoinSingles2All
java -cp bin/ OrderMarkers2
java -cp bin/ LMPlot
java -cp bin/ Pileup2Likelihoods
(java -cp bin/ OutputData)

These are now removed
#java -cp bin/ SeparateIdenticals
#java -cp bin/ JoinSingles2Identicals
#java -cp bin/ ShortPath


How to compile Lep-MAP3:
javac src/*.java -d bin/


(C) 2016-2022, Pasi Rastas, University of Cambridge and University of Helsinki