cecileane / ibpp Goto Github PK

View Code? Open in Web Editor NEW

12.0 4.0 6.0 558 KB

Bayesian species delimitation integrating genes and traits

License: GNU General Public License v3.0

C 100.00%

ibpp's Introduction

iBPP: integration of genes and traits for Bayesian Phylogenetics and Phylogeography

Claudia Solís-Lemus, L. Lacey Knowles and Cécile Ané (2014). Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution 69(2):492-507.
Ziheng Yang and Bruce Rannala (2010). Bayesian species delimitation using multilocus sequence data. PNAS 107:9264–9269. software.

See the version history for potentially new features.

For a Windows executable and instructions, see here.

Installation

Warning: the code compiles but does not work with the more recent gcc compilers.

works well with, for example: gcc v5 (Linux), or clang v7.0.2, clang v12.0.0 (OSX)
compiles (an executable is produced) but doesn't work with gcc v6.1.0 or gcc v7.5.0 (Unbuntu 18.04)

To install and compile on Linux or Mac (with Xcode installed):

download and unzip the package, or clone it using git: git clone https://github.com/cecileane/iBPP.git
navigate to the source directory: cd iBPP/src/
compile with gcc -o ibpp -O3 bpp.c tools.c -lm. On Mac OS X, do clang -o ibpp -O3 bpp.c tools.c -lm to request the Apple compiler clang explicitly. With gcc 4.4.7 to 5.4.0, the option -std=c89 is necessary:

gcc -o ibpp -O3 -std=c89 bpp.c tools.c -lm
move the executable to a directory in your PATH, typically ~/bin/, to run iBPP from anywhere: mv ibpp ~/bin/
check that the executable runs on a very short example:
- navigate to the example folder: cd ../examples/
- then run ibpp: ibpp 5s.analysis.ctl

A simulation tools is also available as part of the package. To get it, compile with the option

gcc -o ibpp-simul -DSIMULATION -O3 bpp.c tools.c -lm

possibly adding the option -std=c89 depending on your compiler.

ibpp's People

Contributors

Stargazers

Watchers

Forkers

simjoly zefeng-wu ariadnesabbag crsl4 tarunocean phebianodufuwa

ibpp's Issues

time reset.file format error

Hi Cecileane,

I am running ibpp analyses for different subsets of my data. From those, I have encountered similar error message as below. I would appreciate if you can point out a direction of solving this problem. Thanks!
Yong-Chao

This is a message after finishing MCMC:

spnode 7: P(tau < 2e-005) = 0.87317 P(tau < 0.0002) = 0.99886 (LMQRST)
spnode 8: P(tau < 2e-005) = 0.91065 P(tau < 0.0002) = 0.99932 (LM)
spnode 9: P(tau < 2e-005) = 0.96279 P(tau < 0.0002) = 0.99999 (QRST)
spnode 10: P(tau < 2e-005) = 0.98014 P(tau < 0.0002) = 1.00000 (QRS)
spnode 11: P(tau < 2e-005) = 0.98491 P(tau < 0.0002) = 1.00000 (QR)

Summarizing, time reset.file format error: 15 fields in line 2 while 12 fields in first line.
Error: error in scanfile().

C:\Users\USER\Desktop\New folder>

Error: ghost pattern?

Hi! I'm encountering this error ("Error: ghost pattern?") whenever I include sequences to the analyses, and I have no clue what is causing it. I can run iBPP without big problems using only morphological input. The error is happening even with the examples that come with the code (iBPP/examples). Entering the directory examples and running "ibpp lizard.bpp.ctl" will return the following output (I've activated the "noisy" option, hoping it could provide useful information):

iBPP v2.1.3 (BPPv2.1 May 2011) integrated with traits, January 2017

Copyright (C) 2014-2017 C. Solis-Lemus and C. Ane, based on Z. Yang's BP&P.

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

Reading options from lizard.bpp.ctl..
rj algorithm 0: new theta from sliding window with c = 5.00
5 species:  tri (4) cow (3) con (4) und (5) woo (1)
(((tri, cow), con), (und, woo));

pop by pop table showing node numbers in species tree

                      1  2  3  4  5  6  7  8  9
species  1 tri        1  0  0  0  0  1  1  1  0
species  2 cow        0  1  0  0  0  1  1  1  0
species  3 con        0  0  1  0  0  1  1  0  0
species  4 und        0  0  0  1  0  1  0  0  1
species  5 woo        0  0  0  0  0  1  0  0  1
species  6 tricowconundwoo   0  0  0  0  0  1  0  0  0
species  7 tricowcon   0  0  0  0  0  1  1  0  0
species  8 tricow     0  0  0  0  0  1  1  1  0
species  9 undwoo     0  0  0  0  0  1  0  0  1

8 theta parameters (populations) in the order:  1 (tri)  2 (cow)  3 (con)  4 (und)  8 (tricow)  7 (tricowcon)  9 (undwoo)  6 (tricowconundwoo)
4 species divergence times in the order:  6 (tricowconundwoo)  7 (tricowcon)  8 (tricow)  9 (undwoo)

Reading Individual-Species map (Imap) from lizard.Imap.txt
Individual -> Species map:  1 1 1 1 2 2 2 3 3 3 3 4 4 4 4 4 5

Reading sequence data..  1 loci

ns = 17         ls = 594
Reading sequences, sequential format..
Counting site patterns..  0:00
          42 patterns at      594 /      594 sites (100.0%),  0:00

Error: ghost pattern?.

Error: strange here

Hi Cecile,

I'm running a ibpp analysis and got the following error:

Error: strange here

I saw this once before too. On my latest analysis I was running without data (useseqdata=0, usetraitdata=0), which may be relevant. I'm also curious that the delimitation didn't change over the course of this analysis. Should I be changing some other prior having to do with the node-collapsing/reversible jump frequency? Thanks in advance for your help!

stdout progress before crash:

...
  5% 0.69 0.30 0.29 0.27 0.33 1.00  24 0.0000 10000  0.01214 17:28
 10% 0.69 0.33 0.26 0.30 0.33 1.00  24 0.0001 10000  0.01006 26:15
 15% 0.68 0.30 0.25 0.40 0.33 1.00  24 0.0001 10000  0.00723 34:55
 20% 0.68 0.29 0.23 0.46 0.33 1.00  24 0.0001 10000  0.00689 43:34
 25% 0.68 0.28 0.23 0.49 0.33 1.00  24 0.0001 10000  0.00666 52:13
 30% 0.68 0.27 0.22 0.52 0.33 1.00  24 0.0001 10000  0.00717 1:00:49
 35% 0.68 0.26 0.23 0.51 0.33 1.00  24 0.0001 10000  0.00871 1:09:22
 40% 0.68 0.26 0.23 0.51 0.33 1.00  24 0.0001 10000  0.00898 1:17:57
 45% 0.68 0.25 0.24 0.51 0.33 1.00  24 0.0000 10000  0.00858 1:26:33
 50% 0.68 0.26 0.24 0.50 0.33 1.00  24 0.0001 10000  0.00787 1:35:19
 55% 0.68 0.27 0.23 0.50 0.33 1.00  24 0.0001 10000  0.00723 1:44:04
 60% 0.68 0.26 0.23 0.51 0.33 1.00  24 0.0001 10000  0.00673 1:52:45

Error: strange here.

the ctl file

seed = 195210
seqfile = /ysm-gpfs/home/de243/Canarium-GBS/analysis_bpp/example2.ibpp.seq.txt
Imapfile = /ysm-gpfs/home/de243/Canarium-GBS/analysis_bpp/example2.ibpp.imap.txt
mcmcfile = /ysm-gpfs/home/de243/Canarium-GBS/analysis_bpp/example2.ibpp.mcmc.txt
outfile = /ysm-gpfs/home/de243/Canarium-GBS/analysis_bpp/example2.ibpp.out.txt
traitfile = /ysm-gpfs/home/de243/Canarium-GBS/analysis_bpp/example2.ibpp.traits.txt
nloci = 200
cleandata = 0
speciesdelimitation = 1 1 1 1
ntraits = 27
nindT = 36
usetraitdata = 0
useseqdata = 0
nu0 = 0
kappa0 = 0
species&tree = 6 A B C D E F
                 9 4 3 6 2 13
                 ((((D,C),B),(E,F)),A);
thetaprior = 2 200
tauprior = 2 200 1
finetune = 1: 100.0 0.0001 0.0001 0.0001 0.1 0.001 0.1 0.1
print = 1 0 0 0
burnin = 10000
sampfreq = 2
nsample = 100000

cecileane / ibpp Goto Github PK

ibpp's Introduction

iBPP: integration of genes and traits for Bayesian Phylogenetics and Phylogeography

Installation

ibpp's People

Contributors

Stargazers

Watchers

Forkers

ibpp's Issues

time reset.file format error

Error: ghost pattern?

Error: strange here

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent