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Fast and Robust Phylogeny-Aware Multiple Sequence Alignment
- tandem repeat unit insertions and deletions
PLEASE NOTE: this repository is ARCHIVED and UNMAINTAINED. All further development is done at:
https://github.com/acg-team/ProGraphMSA
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The easiest way to run ProGraphMSA with the recommended command line parameters
is to use the wrapper script "ProGraphMSA+TR.sh" included in this package. Just run
./ProGraphMSA+TR.sh
or
./ProGraphMSA+TR.sh -o
ProGraphMSA+TR will run using ML distances, the WAG model, and will output an
alignment in FASTA format. Further it will use T-REKS from the file T-Reks.jar
to detect tandem repeats. To use TRUST adjust the installation path in
trust2treks.py and run
./ProGraphMSA+TR.sh --custom_tr_cmd trust2treks.py
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USAGE:
./ProGraphMSA [--ancestral_seqs] [--all_trees] [-i ] [-T] [-I]
[-M] [-m] [-a] [-C ] [-F] [--custom_model ] [-w]
[-c ] [-r] [--custom_tr_cmd ] [--trd_output
] [--read_repeats ] [-R] ...
[--repalign] [--repeat_indel_ext ]
[--repeat_indel_rate ] [-A] [-P ] [-p
] [-D ] [-d ] [-x ]
[-s ] [-l ] [-E ] [-e
] [-g ] [-f] [--dna] [--codon] [--topology
] [-t ] [-o ] [--]
[--version] [-h]
Tandem-repeat related parameters:
=================================
-R, --repeats
use T-REKS to identify tandem repeats
--custom_tr_cmd
custom command for detecting tandem-repeats
--trd_output
write TR detector output to file
--read_repeats
read TR detector output from file
--repalign
re-align detected tandem repeat units
--repeat_indel_ext
repeat indel extension probability
--repeat_indel_rate
insertion/deletion rate for repeat units (per site)
Guide tree, distances, and substitution model:
==============================================
-i , --iterations
number of iterations re-estimating guide tree [default: 2]
-m, --mldist
use distances estimated by a Maximum-Likelihood method
-a, --nwdist
estimate initial distance tree from Needleman-Wunsch alignments
-D , --max_dist
maximum distance for alignment
-F, --estimate_aafreqs
estimate equilibrium amino acid frequencies from input data
-w, --darwin
use model of evolution from Darwin (GONNET matrix and different indel model parameters, otherwise WAG will be used)
--custom_model
custom substitution model in qmat format
-c , --cs_profile
path to library of context-sensitive profiles (we distribute a copy in the 3rd_party folder)
-A, --no_force_align_m
do not force alignment of initial Methionine
Parameters for adjusting the indel model:
=========================================
-l , --edge_halflife
edge half-life (evolutionary distance at which the probability of re-using an unsused graph is halved)
-E , --end_indel_prob
probability of mismatching sequence ends (set to -1 to disable this feature)
-e , --gap_ext
gap extension probability
-g , --indel_rate
insertion/deletion rate
Input/Output:
=============
-f, --fasta
output fasta format (instead of stockholm)
-t , --tree
initial guide tree
-o , --output
Output file name
-I, --input_order
output sequences in input order (default: tree order)
--dna
align DNA sequence
--codon
align DNA sequence based on a codon model
--ancestral_seqs
output all ancestral sequences
(required) input sequences
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| _ \ || | | / _` | | ' \/ _` | | _| '_/ _ \ ' \ (_-=2.8 (http://www.cmake.org)
tclap >=1.1.0 (http://tclap.sourceforge.net)
Eigen 2.0.x or 3.0.x (http://eigen.tuxfamily.org)
on Debian/Ubuntu you can install these programs/libraries with:
sudo apt-get install cmake libtclap-dev libeigen2-dev
Then perform the following command to configure/build/install ProGraphMSA:
cd BUILD
ccmake .. (press "c" to configure and "g" to generate the Makefile, see below
for additional configuration options)
make ProGraphMSA
make install
Additional CMake configuration options (in "ccmake .."):
EIGEN2_INCLUDE_DIR: set this to the path, where Eigen is installed, if you use
Eigen 3.0.x or if Eigen has been installed at a non-default
location (default location: /usr/include/eigen2)
WITH_EIGEN3: set this to ON, if you want to compile ProGraphMSA with
Eigen 3.0.x
CMAKE_CXX_FLAGS: add options for the C++ compiler, like optimization flags,
or additional search paths for include files (-I )
WITH_SSE: disable this option, if you build ProGraphMSA for a machine
that does not support SSE2