LAMARC

version 2.1.2b
Lamarc is a program for doing Likelihood Analysis with Metropolis Algorithm using Random Coalescence. Lamarc estimates effective population sizes, population exponential growth rates, a recombination rate, and past migration rates for one to n populations assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes.

• written in C++
• LINUX
• Mac OSX
• Windows

• DNA sequence
• RNA sequence
• SNP
• Microsatellites
• electrophoretic data

can convert PHYLIP, RECOMBINE and MIGRATE files to a LAMARC XML file

• surrounded by <lamarc> and </lamarc>

Data section:
contains the actual molecular data, and additional information used to interpret it

• enclosed in <data> tags
• <region>:
  • divides molecular data into “regions”
  • available genetic information that is closely linked on the same chromosome and has a known map
  • Use multiple regions for data composed of several disconnected bits or bits whose connections are not known
  • region's name: optional name attribute
• <effective-popsize> (optional):
  • specify a different relative effective population size for each <region>
• <spacing>:
  • Information about the relative position of segments
• <block>:
  • Each segment is indicated by this tag
  • give information about the position of the segment itself and the positions of the markers within the segment
  • <length>: indicates the total length of the segment (important for SNPs)
  • <map-position>: gives the position of this segment on an overall map of the region (the point at which sequencing or scanning began)
  • <locations>: a list of marker positions within the region
  • <offset>: the origin of the segment's numbering system with respect to the boundaries of the region
• <population>:
  • Within each region you can list various populations
  • if you list <population> tags under more than one region, they will be matched by means of their name attributes, so the names are not optional
  • <individual>: represents all the data for that region that comes from a single biological individual (one or more sets). Individuals can have a name attribute (optional)

Kuhner, M. K., 2006 “LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters.” Bioinformatics 22(6): 768-770.