During a linkage analysis project, it can often be quite difficult to get one’s data in the proper format desired by each different computer program. Not only must the data be converted to the proper format, but also the loci must be reordered into their proper order. To address this problem, we created Mega2.
A typical linkage-analysis study requires information regarding
pedigree structure, trait phenotypes, and genetic marker data. One
commonly used data format is the one used by the LINKAGE programs
(Lathrop and Lalouel 1984; Lathrop et al. 1986; Lathrop and Lalouel
1988); these formats are described in detail in the LINKAGE User's
Guide at
LINKAGE-format files typically come in pairs: the “datain.dat” contains the locus information (disease model, allele frequencies, numbers of alleles, etc.), while the “pedin.dat” contains the pedigree structure information and phenotypes. However, the original LINKAGE-format made no provisions for locus names nor for marker map information. So Mega2 uses as input a trio of files which remedy these omissions:
1) the locus file modified to contain locus name information;
2) the pedigree file; and
3) the map file.
Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts).
Mega2 is currently structured so that the user proceeds through a series of menus, making choices in each one (or accepting the default values), until the desired output files are created. After the desired output files are created, Mega2 exits. It can also be run in a "hands-free" mode, using a control file to specify these choices.