ERaBLE: Evolutionary Rates and Branch Lengths Estimation
Fast and accurate branch lengths estimation for phylogenomic trees.
Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel J.P. Douzery and Fabio Pardi. BMC Bioinformatics. 2016, 17:23.
Please cite THIS paper if you use ERaBLE.
Please cite THIS paper if you use ERaBLE.
User guide:
1 Availability
Binaries and source code: DownloadsBug report: If you ever come across an issue, please feel free to report it sending an email to manuel.binet AT lirmm DOT fr
2 Installing ERaBLE
2.1 Compilation for UNIX/Linux/Mac
In a command-line window, go to the directory that contains the archive erable*.tar.gz and type:-
tar -xzf erable*.tar.gz
cd erable
./configure
make
sudo make install
2.2 Installation for Windows
Copy the files erable.exe and erable.bat in the same directory. Modify the command line in erable.bat with your favorite text editor. To launch ERaBLE, click on the icon corresponding to erable.batAlternatively you can compile the sources with ./configure and make.
3 Input files
ERaBLE requires at least two input files: one matrices file and one tree topology file.The matrices file contains a list of m distance matrices in PHYLIP format (lower triangular or square); the value of m must be given at the beginning of the file (see example below). The length of the sequences (called N_k in the following) must follow the number of taxa as done in PHYLIP alignment files. If the length of the sequences are not available, you can set the same length value (e.g. 1) for all the matrices. The tree topology file contains an unrooted, binary tree topology in NEWICK format whose branch lengths - if specified - will be ignored. Comments inside the input files start with the # character for Windows and Unix. For Unix version you can use // characters too.
An example of input matrices file containing square distance matrices: input_matrices.txt
//comment: Gene names "%names" are optional
3
%Gene 43
4 381
Tax10 0.00000000 0.63692700 1.18140000 1.07080000
Tax3 0.63692700 0.00000000 0.70195800 0.59136000
Tax20 1.18140000 0.70195800 0.00000000 0.61216600
Tax4 1.07080000 0.59136000 0.61216600 0.00000000
%Gene 60
4 210
Tax14 0.00000000 0.11026300 0.29855000 0.27683700
Tax3 0.11026300 0.00000000 0.21525100 0.19353800
Tax20 0.29855000 0.21525100 0.00000000 0.15977400
Tax4 0.27683700 0.19353800 0.15977400 0.00000000
%Gene 69
4 590
Tax34 0.00000000 0.39659600 0.42909900 0.42292600
Tax14 0.39659600 0.00000000 0.46365800 0.45748400
Tax20 0.42909900 0.46365800 0.00000000 0.28217300
Tax4 0.42292600 0.45748400 0.28217300 0.00000000
An example of input tree toplogy file with branch lengths (ignored): input_tree_topology.nwk
(Tax10:0.51144,(Tax34:0.19411,(Tax20:0.19064,Tax4:0.15564):0.09995):0.09856,(Tax14:0.10233,Tax3:0.03293):0.01914);
4 Output files
ERaBLE outputs two outfiles:
- The topology in NEWICK format with the branch lengths computed by ERaBLE with the suffix ".lengths.nwk"
- The gene rates with the suffix ".rates.txt"
The outfiles of ERaBLE for: erable -i input_matrices.txt -t input_tree_topology.nwk
((Tax10:0.338333578449,(Tax34:0.233436677569,(Tax20:0.197509459236,Tax4:0.16370288841):0.134789424385):0.0372630086088)
:0.0329947660905,Tax3:0.0194998053449,Tax14:0.20724052087);
gene rate
Gene 43 1.62969
Gene 60 0.486296
Gene 69 0.776216
5 Program usage
ERaBLE's usage is :
erable -i <infile(matrices)> -t <infile(tree)> <options>
options:
-o <outfile>;
-w <weights> ols, wseq (default), user infile weights;
-m <system solving method> ldlt (Cholesky without square root calcul(default)), llt (Cholesky), QR , LU;
-p <integer>: output precision (default 12 significant digits);
-c <constraint> ols, cseq, nksumdist (default);
An example of syntax:
$ ./erable -i input_matrices.txt -t input_tree_topology.nwk
A run with this syntax estimates the branch lengths of the reference topology given in the file "input_tree_topology.nwk", and the gene rates,
using the collection of distance matrices given in the file "input_matrices.txt". The branch lengths are given in the outfile with the suffix ".lengths.nwk"
and the gene rates in the outfile with the suffix ".rates.txt".
The parameters can be specified as follows:
- -i <infile(matrices)>
<infile(matrices)> is the name of the input matrices file in PHYLIP format.
- -t <infile(tree)>
<infile(tree)> is the name of the input tree topology file in NEWICK format.
- -o <outfile>
<outfile> is the name to redirect or rename the branch lengths output file. By default
the output file is in the directory of the input matrices file.
- -w <weights>: ols , wseq (default), user infile weights;
<weights> is the user infile weights in PHYLIP format or one of the above options (ols ...).
- ols: w_{ij}^{(k)}=1
- wseq: w_{ij}^{(k)}=N_k (where N_k is the length of the sequences)
- <infile(weights)>: to use weigths of the user infile weights <infile(weights)> in PHYLIP format.
An example of input weights file:
3
4
Tax10 0.00000000 10.0000000 10.0000000 10.0000000
Tax3 10.0000000 0.00000000 9.00000000 9.00000000
Tax20 10.0000000 9.00000000 0.00000000 8.00000000
Tax4 10.0000000 9.00000000 8.00000000 0.00000000
4
Tax14 0.00000000 50.0000000 50.0000000 50.0000000
Tax3 50.0000000 0.00000000 40.0000000 40.0000000
Tax20 50.0000000 40.0000000 0.00000000 50.0000000
Tax4 50.0000000 40.0000000 50.0000000 0.00000000
4
Tax34 0.00000000 10.0000000 10.0000000 10.0000000
Tax14 10.0000000 0.00000000 10.0000000 10.0000000
Tax20 10.0000000 10.0000000 0.00000000 10.0000000
Tax4 10.0000000 10.0000000 10.0000000 0.00000000
- -m <system solving method>: ldlt=Cholesky without square root calcul(default), llt=Cholesky, QR , LU.
to choose the method to solve the system, see Eigen for more details.
- -p <integer>: output precision (default=12).
<integer> is the number of significant digits to display in the outfiles.
- -c <constraint>: ols, cseq, nksumdist.
to choose the constraint on the scale factors:
\sum_{k=1}^mZ_k\alpha_k=\sum_{k=1}^mZ_k
- ols:
Z_k=1
- cseq:
Z_k=N_k
- nksumdist (default):
Z_k=N_k\sum_{ij}\delta_{ij}^{(k)}
((Tax10:0.338333578449,(Tax34:0.233436677569,(Tax20:0.197509459236,Tax4:0.16370288841):0.134789424385):0.0372630086088)
:0.0329947660905,Tax3:0.0194998053449,Tax14:0.20724052087);
gene rate
Gene 43 1.62969
Gene 60 0.486296
Gene 69 0.776216
erable -i <infile(matrices)> -t <infile(tree)> <options>
options:
-o <outfile>;
-w <weights> ols, wseq (default), user infile weights;
-m <system solving method> ldlt (Cholesky without square root calcul(default)), llt (Cholesky), QR , LU;
-p <integer>: output precision (default 12 significant digits);
-c <constraint> ols, cseq, nksumdist (default);
$ ./erable -i input_matrices.txt -t input_tree_topology.nwk
<infile(matrices)> is the name of the input matrices file in PHYLIP format.
<infile(tree)> is the name of the input tree topology file in NEWICK format.
<outfile> is the name to redirect or rename the branch lengths output file. By default the output file is in the directory of the input matrices file.
<weights> is the user infile weights in PHYLIP format or one of the above options (ols ...).
- ols: w_{ij}^{(k)}=1
- wseq: w_{ij}^{(k)}=N_k (where N_k is the length of the sequences)
- <infile(weights)>: to use weigths of the user infile weights <infile(weights)> in PHYLIP format.
An example of input weights file:
3 4 Tax10 0.00000000 10.0000000 10.0000000 10.0000000 Tax3 10.0000000 0.00000000 9.00000000 9.00000000 Tax20 10.0000000 9.00000000 0.00000000 8.00000000 Tax4 10.0000000 9.00000000 8.00000000 0.00000000 4 Tax14 0.00000000 50.0000000 50.0000000 50.0000000 Tax3 50.0000000 0.00000000 40.0000000 40.0000000 Tax20 50.0000000 40.0000000 0.00000000 50.0000000 Tax4 50.0000000 40.0000000 50.0000000 0.00000000 4 Tax34 0.00000000 10.0000000 10.0000000 10.0000000 Tax14 10.0000000 0.00000000 10.0000000 10.0000000 Tax20 10.0000000 10.0000000 0.00000000 10.0000000 Tax4 10.0000000 10.0000000 10.0000000 0.00000000
to choose the method to solve the system, see Eigen for more details.
<integer> is the number of significant digits to display in the outfiles.
to choose the constraint on the scale factors:
\sum_{k=1}^mZ_k\alpha_k=\sum_{k=1}^mZ_k
- ols:
Z_k=1
- cseq:
Z_k=N_k
- nksumdist (default):
Z_k=N_k\sum_{ij}\delta_{ij}^{(k)}
Contact: Webmaster, LIRMM.
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