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INSTALL GSL FOR MAC FOR MAC OSX
INSTALL GSL FOR MAC MAC OS X
INSTALL GSL FOR MAC INSTALL
INSTALL GSL FOR MAC ARCHIVE
INSTALL GSL FOR MAC CODE

ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. It is maintained by Ziheng Yang and distributed under the GNU GPL v3. PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Phylogenetic analysis by maximum likelihood (PAML) Maximum likelihood implementation of an isolation-with-migration model for three species. Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow.

INSTALL GSL FOR MAC MAC OS X

On Mac OS X and Windows you need a compiler with OpenMP support. This should work out-of-the-box on current Linux systems with the GNU tool chain. Gcc -O3 -DUSE_GSL -I/usr/local/include -L/usr/local/lib -o 3s -fopenmp 3s.c tools.c lfun3s.c -lm -lgsl -lgslcblas Use the following command (adapted to your system) to compile the source code: You can use 3s as it is, without any additional libraries installed.

INSTALL GSL FOR MAC CODE

The source code is available here Downloads and Installation

It can take advantage of multi-core architectures to speed up computation.

By default, it uses an asymmetric IM model with θ 1 ≠ θ 2 and M 12 ≠ M 21.

It allows the use of loci with arbitrary configurations (such as 123, 112, 113, 12, etc.).

2017) includes several improvements over previous versions: The program 3s implements likelihood ratio tests to test for gene flow between two closely related species. (2020) A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis. Please also cite the following papers depending on the method you use:įlouri T., Jiao X., Rannala B., Yang Z. (2018) Species Tree Inference with BPP using Genomic Sequences and the Multispecies Coalescent. Citing BP&Pįlouri T., Jiao X., Rannala B., Yang Z. Please download from Bruce’s group web site. You can use this to prepare the bpp control files, and also read in the species trees in the MCMC sample file, produced by either bpp3.4 or bpp4. The executables are for Windows and Mac OSX.

This may not be working with the new versions of bpp, such as 3.4 and 4.īruce Rannala has written another BPPgui.

INSTALL GSL FOR MAC INSTALL

You install (unpack and compile) the current version of bpp first, unpack the GUI bppX, and then go to Function-Configuration to specify the folder name for the bpp files. The compiled executables are here for Windows, Mac OSX, and linux. Bo Xu has written a graphics user interface for BP&P, called bppX. If you have questions about either bpp3.4 or bpp4, please post them at the google bpp discussion site.īP&P replaces the old program MCMCcoal, which implements the Bayesian method of Rannala & Yang (2003) and Burgess & Yang (2008).

INSTALL GSL FOR MAC FOR MAC OSX

Download bpp3.4.macosx.tgz (source code and executables for mac osx 7 and later).If Internet Explorer changes the file extension to.

INSTALL GSL FOR MAC ARCHIVE

The archive bpp3.4a.tgz includes the source code for all platforms, as well as executables for Windows.A tutorial of BPP for species tree estimation and species delimitation. BP&P version 3 source code and executables for mac osx 7 and later.

The source code for the previous BP&P v3.4 is available in the links below: Please also read the 2015 tutorial on BPP 3.4. Species tree inference with BPP using genomic sequences and the multispecies coalescent.

BP&P version 4 installation instructions.

BP&P version 4 github repository for source code.

The same control file works for both versions although bpp4. Also the multispecies-coalescent-with-introgression (MSci) model is implemented in bpp4 only, and not in bpp3.4. We suggest that you get bpp version 4 as it contains all the functionalities of version 3.4, but runs much faster and supports multiple threads.

The analyses may include estimation of population size (theta’s) and species divergence times (tau’s), species tree estimation, species delimitation, and estimation of cross-species introgression intensity. The BP&P program implements a series of Bayesian inference methods under the multispecies coalescent model with and without introgression.

Phylogenetic analysis by maximum likelihood (PAML)īP&P: Bayesian analysis of genomic sequence data under the multispecies coalescent model.

BP&P: Bayesian analysis of genomic sequence data under the multispecies coalescent model.