Commit def050e2 authored by Fabian Klötzl's avatar Fabian Klötzl

Imported Upstream version 0.9.4.1

parent 85bea24c
# Binary and automatically generated files
*.o
*.a
andi
andi_*
randomSeed.dat
seedms
testRMQ
src/config.h
src/stamp-h1
src/config.hin
src/config.hin~
#docs
docs/doxygen_sqlite3.db
docs/html/*
docs/latex/*
docs/andi.1
*.aux
*.auxlock
*.dep
*.dpth
*.toc
*.out
*.pdf
*.backup
*.bbl
*.blg
!andi-manual.pdf
*.in
!docs/andi.1.in
!docs/manual/version.tex.in
docs/manual/version.tex
*.log
**/Makefile
configure.scan
config.status
depcomp
install-sh
aclocal.m4
**/.deps/
autom4te.cache/
README
ChangeLog
missing
compile
configure
ar-lib
src/.dirstamp
# test files
*.fasta
cachegrind*
callgrind*
test.trs
test-driver
test_esa
test_seq
test_fasta
*.trs
# Coverage
*.gcda
*.gcno
*.gcov
andi.sublime-*
# for legacy git only:
libs/RMQ/.deps/
libs/RMQ/Makefile
Makefile
# Profiling:
gmon.out
profile
language: cpp
compiler:
- gcc
before_install:
- sudo pip install cpp-coveralls
- sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
- sudo apt-get update -qq
- if [ "$CXX" = "g++" ]; then sudo apt-get install -qq g++-4.8; fi
- if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
- sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90
- sudo apt-get install libglib2.0-dev
- wget https://libdivsufsort.googlecode.com/files/libdivsufsort-2.0.1.tar.gz
- tar -xzvf libdivsufsort-2.0.1.tar.gz
- cd libdivsufsort-2.0.1
- mkdir build
- cd build
- cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="/usr/local" ..
- make
- sudo make install
- cd $TRAVIS_BUILD_DIR
- export LD_LIBRARY_PATH=/usr/local:$LD_LIBRARY_PATH
script:
- export LD_LIBRARY_PATH=/usr/local/lib:/usr/local:$LD_LIBRARY_PATH
- export OMP_NUM_THREADS=4
- autoreconf -fvi -Im4
- ./configure --enable-unit-tests CFLAGS='-fprofile-arcs -ftest-coverage' CXXFLAGS='-fprofile-arcs -ftest-coverage'
- make
- make check
- make distcheck
- tar xzvf andi-*.tar.gz
- cd andi-*
- ./configure --enable-unit-tests --without-libdivsufsort
- make
- make check
- cd ..
after_success:
- coveralls --exclude libdivsufsort-2.0.1 --exclude libs --exclude test --gcov `which gcov-4.8` --gcov-options '\-lp'
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[![Build Status](https://travis-ci.org/EvolBioInf/andi.svg?branch=master)](https://travis-ci.org/EvolBioInf/andi) [![Coverage Status](https://coveralls.io/repos/EvolBioInf/andi/badge.svg?branch=master)](https://coveralls.io/r/EvolBioInf/andi?branch=master)
# About
This is the `andi` program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because `andi` does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
This readme covers all necessary instructions for the impatient to get `andi` up and running. For extensive instructions please consult the [manual](andi-manual.pdf).
# Build Instructions
For the latest [stable release](https://github.com/EvolBioInf/andi/releases) of `andi` download the tar ball. If you'd like to contribute to this software, feel free to create a fork of our [git repository](https://github.com/EvolBioInf/andi) and send pull requests.
## Prerequisites
This program has the following external dependency: [libdivsufsort](https://code.google.com/p/libdivsufsort/). Please make sure you installed `libdivsufsort` before attempting a build. If you did get the source, not as a tarball, but straight from the git repository, you will also need the autotools. Run `autoreconf -i` to generate the configure script and continue with the next step.
## Compiling
Assuming you have installed all prerequisites, building is as easy as follows.
$ ./configure
$ make
$ make install
Excessive build instructions are located in `INSTALL`. If the build was successful you can get the usage instructions via `--help` or the man page.
$ andi --help
$ man andi
You can use simply `andi` with your genomes in `FASTA` format.
$ andi S1.fasta S2.fasta
2
S1 0.0 0.1
s2 0.1 0.0
From this distance matrix the phylogeny can be inferred via neighbor-joining. Check the [manual](andi-manual.pdf). for a more thorough description.
# Links and Additional Resources
The release of this software is accompanied by a paper from [Haubold et al.](http://bioinformatics.oxfordjournals.org/content/31/8/1169). It explains the used *anchor distance* strategy in great detail. The `maf2phy.awk` script used in the validation process is located under `scripts`. Simulations were done using our own [simK](http://guanine.evolbio.mpg.de/bioBox/) tool.
## Data Sets
1. 29. E. coli strains: [data](http://guanine.evolbio.mpg.de/andi/eco29.fasta.gz)
2. 109 E. coli ST131 strains ([paper](http://www.pnas.org/content/early/2014/03/28/1322678111.abstract)):
* [99 newly sequenced strains](https://github.com/BeatsonLab-MicrobialGenomics/ST131_99)
* [10 previously published strains](http://guanine.evolbio.mpg.de/andi/st131_extra.tgz)
3. 3085 Streptococcus pneumoniae strains ([paper](http://www.nature.com/ng/journal/v46/n3/full/ng.2895.html)): ftp://ftp.sanger.ac.uk/pub/pathogens/Streptococcus/pneumoniae/Maela_assemblies.tgz
## License
Copyright © 2014, 2015 Fabian Klötzl
License GPLv3+: GNU GPL version 3 or later.
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at <http://gnu.org/licenses/gpl.html>.
Some files may be licensed differently.
## Contact
In case of bugs or unexpected errors don't hesitate to send me a mail: kloetzl@evolbio.mpg.de
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AC_INIT([andi], [0.9.4])
AC_INIT([andi], [0.9.5-beta])
AM_INIT_AUTOMAKE([-Wall foreign ])
AC_CONFIG_MACRO_DIR([m4])
......@@ -83,7 +83,7 @@ AC_HEADER_STDBOOL
# non-null pointer. This breaks the build on systems using uClibc, including
# my laptop.
# As requesting zero bytes is not useful, and implementation-defined behaviour,
# I should be avoided in the first place. Thus I really don't need these checks.
# it should be avoided in the first place. Thus I really don't need these checks.
AC_CHECK_FUNCS([floor pow sqrt strdup strerror])
AC_CHECK_FUNCS([strndup])
......
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\newcommand{\version}{VERSION}
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