Sebastian E. Ramos-Onsins*, Aaron Windsor**
Max-Planck Institute of Chemical Ecology
*Universitat de Barcelona; **Duke University
MANVa : Multilocus Analysis of
Current Released Version: 0.982beta
(March 14th, 2008)
This package contains the application MANVa and the group of Python scripts QueryGbkPipe.
1. The application program MANVA is
2. The Python
scripts QueryGbkPipe.tar.bz2 are designed to:
empirical data from a single population and an outgroup species
(if included). It is designed for analyzing a large number of
- Subset of
regions can be analyzed (synonymous, silent, introns, etc). A
GFF file associated to each alignment can be provided.
multilocus coalescent simulations conditioned on:
population mutation rate theta (4Nu, where N is the effective
population size and u is the mutational rate).
population recombination rate theta (4Nr, where r is the recombination
recurrent mutations (multiple hits).
levels of variation by maximum likelihood for the multilocus set.
multilocus analyses: calculate probabilities and confidence intervals
for the observed data
when comparing with simulated data, and calculate percentiles for
simulated data.A wide number of statistical tests and neutrality tests
are calculated (Tajima's D, Fu and Li's D and F, Fay and Wu's H, Wall's
B and Q, Ramos and Rozas' R2, etc...). Histogrames for the observed and
simulated data are also obtained. Kolmogorov-Smirnov tests are
calculated to compare observed vs simulated data. Multilocus
statistics are the average and the variance for each statistic. Sign
tests are also performed.
This program is
based on a previous version of Hudson's coalescent program ms (Hudson,
2002) and modified for the above purposes.
this scripts take the output from a QGP project and creates GFF
annotations for your query FASTA files.
- Currently, the scripts
only annotates 'exons'. The scripts produce three directories:
gff_support, which contains supporting data;
gff_with_alignments and gff_for_MANVa, both of which contain multiFASTA
alignments (*.fas) and an accompanying tab-delimited text file with the
GFF annotation for a given alignment. The files in 'gff_for_MANVa'
following the naming convention required by the MANVa program.
Download MANVa package: including source files,
readme file, an example and the executables:
- This program is
distributed under the GNU General
questions, comments and bug reports to Sebastian E. Ramos-Onsins at:
since February, 2007.
March 18th, 2008