GAPL Version 1.2 updated

GAPL is freely-available public software, capable of building high-density genetic linkage maps and mapping quantitative trait loci (QTL) in pure line populations derived from four-way or eight-way crosses. The software is project based and has user-friendly interfaces. Version 1.2 of the software was released in September 2018, and updated in July 2019.

Four fully implemented functionalities in GAPL v1.2 are: (1) SNP: Converting the SNP genotyping data to the software format (i.e. from AA, TT, CC, GG, AT, AC, AG, TC, TG, GT to A, B, H. SNP genotypes of the four or eight inbred parent are needed to use this functionality); (2) BIN: Binning of redundant markers; (3) PLM: Construction of genetic linkage maps in multi-parental pure-line populations; (4) PLQ: Gene detection in multi-parental pure-line populations.

What’s updated?

1. In functionality PLM, the estimated recombination frequency and LOD score were recorded in a temporary external file, in order to increase the capability to handle the large number of markers. In current version, the maximum number of markers can reach 20,000 to 40,000. For markers more than 10,000, we suggest to use functionality BIN to remove the redundancy.

2. In functionality PLM, ordering algorithm was optimized.

3. Both 32-bit and 64-bit versions were provided.