Bug#857874: ITP: mptp -- single-locus species delimitation
- Date: Wed, 15 Mar 2017 22:43:09 +0100
- From: Andreas Tille <tille@xxxxxxxxxx>
- Subject: Bug#857874: ITP: mptp -- single-locus species delimitation
Owner: Andreas Tille <tille@xxxxxxxxxx>
* Package name : mptp
Version : 0.2.2
Upstream Author : Paschalia Kapli, a.o.
* URL : https://github.com/Pas-Kapli/mptp
* License : Affero
Programming Lang: C
Description : single-locus species delimitation
Implementation of a fast species delimitation method, based on PTP
(Zhang et al. 2013) with a 64-bit multi-threaded design that handles
very large datasets.
The tool mPTP can handle very large biodiversity datasets. It implements
a fast method to compute the ML delimitation from an inferred
phylogenetic tree of the samples. Using MCMC, it also computes the
support values for each clade, which can be used to assess the
confidence of the ML delimitation.
ML delimitation mPTP implements two flavours of the point-estimate
solution. First, it implements the original method from (Zhang et al.
2013) where all within-species processes are modelled with a single
exponential distribution. mPTP uses a dynamic programming implementation
which estimates the ML delimitation faster and more accurately than the
original PTP. The dynamic programming implementation has similar
properties as (Gulek et al. 2010). See the wiki for more information.
The second method assumes a distinct exponential distribution for the
branching events of each of the delimited species allowing it to fit to
a wider range of empirical datasets.
MCMC method mPTP generates support values for each clades. They
represent the ratio of the number of samples for which a particular node
was in the between-species process, to the total number of samples.
Remark: This package will be maintained by the Debian Med team at