New version of fastsimcoal2 (ver 2.6)

[Laurent Excoffier]

Hi,

I am very pleased to announce that a new version (2.6.0.3) of fastsimcoal2 is available on our web site 

http://cmpg.unibe.ch/software/fastsimcoal2/

Note that it also corrects a bug that prevented correct parameter optimization in some particular cases, which was present in ver 2.6.0.2 released on October 9th (thanks to Rasmus Heller for signalling this problem)

The new version implements the following changes:

1.     Simple implementation of individual inbreeding

·       The average inbreeding coefficient of individuals in a population can now be specified as a third optional parameter in the sample size definition. In this case, the sample age needs to be defined (set to zero in most applications), as:
<sample size> <sample age> <inbreeding coefficient>

2.     Possibility to define initial parameter values for demographic inference

·       Option -initvalues file.pv , where file.pv lists initial non-complex parameter values to use. This option is mainly useful when computing bootstrap confidence intervals, as it allows one to use less replicates for each bootstrap data set. A *.pv file is now automatically generated after each parameter estimation by fsc26.

3.     Computation of MAF 1D and 2D SFS with option --foldedSFS by simply folding the corresponding unfolded SFS (for compatibility with angsd, where the minor allele is computed separately for each SFS)

4.     Optional faster but approximate log computations with option --logprecision n, where n is a number between 10 and 23 specifying the precision of the computation of logarithms. 23 means full precision and is the default value.

5.     Optional parameter optimization without taking singletons into account specified with option --nosingleton

6.     Syntax changes

·       For parameter optimization,

o -N option has been suppressed, and maximum no. of iteration is now equal to that set by the -n option

o The number of cycles to performed is now fixed and only specified with option -L

o The -l option is now optional and means something different. It is now used to specify the number of cycles where information on monomorphic sites is used. After these initial cycles, likelihood will only be computed (and optimized) on the polymorphic sites. This option needs to be used together with the “reference” keyword in the .est file (see section on est file).

o The -M option is now just a flag mentioning we want to perform parameter estimation from the observed SFS. It should therefore not be followed by any number.

·       Removed -D option to produce output in dadi format, as this is virtually identical to the multidimensional SFS output, barring the header

7.     Implementation of instantaneous bottlenecks with keyword instbot added to historical event definition. Only works in absence of recombination for the moment.

8.   No more warnings if deme size tends to zero or infinity if deme is empty (corrected in ver 2.6.0.3) 

9.     Bug corrections:

·       Expected marginal SFS were not computed when computing expected SFS with FREQ data

·       Wrong likelihoods were computed with option -0

·       No more (hopefully) program crash when using large recombination rates

Please report any bugs or comments on this group

Enjoy

laurent

[peace.wa...@gmail.com]

Dear Laurent,
I do not quite understand the option "--foldedSFS".
Does that means I could generate unfolded SFS (1D or 2D) with ANGSD first, and then fold them with fsc2.6?
Thanks!