Data and programs

K. Liu, S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, "Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees," Science, vol. 324, no. 5934, pp. 1561-1564, 19 June 2009.

Data and Programs

How to open a compressed file

All files are in compressed .tar.bz2 format. To extract a compressed <file>, use the command:

tar xjf <file>

tds executable README

libstdc++-3 is required to run this program.
This program has only been verified to work on
Ubuntu 8.04 LTS "Hardy Heron" for 32-bit processors.
tds was originally developed by Prof. Daniel Huson and
was modified by Prof. Usman Roshan.

tds is available here.

To obtain usage information, run:

./usmantds2 -h

To perform the ultrametricity deviation calculation with parameter <u>, run:

./usmantds2 -id tree -od tree -i <newick tree> -c stretch -cm <u>

To obtain the diameter of a tree, run:

./usmantds2 -id tree -od dist -i <newick tree> -o <output file>

To scale all branch lengths by a constant <factor>:

./usmantds2 -id tree -od tree -i <newick tree> -c scale -cm <factor>

SATe README

The SATe program is located here.
After decompressing that file, read the file in the directory
./sate_dist/README and follow those instructions to run SATe.

Most modern desktop machines should support SATe analysis on smaller
datasets of several hundred taxa and several hundred aligned sites. A
desktop machine with 4 GB main memory and at least 1 GB disk space for
the working directory is recommended for the largest datasets from the
paper and for datasets with similar numbers of taxa and sequence
length. These datasets generally have up to several thousand taxa and
several thousand aligned sites. If you encounter errors while
analyzing datasets with greater numbers of taxa or sequence length
than that, you can use a version of SATe that omits starting
alignments with high memory requirements by using the -s 2 option.

A more user-friendly graphical interface version for
various popular operating systems as well as an online web version of SATe
will be released soon. Details will be posted here as soon as they are available.
A very early command-line-Linux-only build of this alternate version
is being alpha-tested here. Please note that testing is ongoing, and this alternate
version is known to be different from the version used in the journal
paper experiments provided above.

SATe is distributed under the GPLv3 license. This distribution contains
other programs which are licensed under different licenses.
Please see ./sate_dist/LICENSE for more details.

Simulated nucleotide datasets README

There are 37 model conditions, with either 1000, 500, or 100 taxa, and either long, medium, or short gap length types. Each model condition is referred to with the string "<number of taxa><gap length type: L for long, M for medium, S for short><id number>". Each model condition has 20 replicate datasets. For each model condition, an associated compressed file is provided, e.g. 1000L1.tar.bz2 corresponds to model 1000L1. The compressed file contains the 20 replicate datasets for that model condition.

After extracting a compressed file, the directory structure <model condition parameter string>/R<replicate number>/
will have the following files:

rose.tt - Potentially Inferrable Model Tree, or PIMT, (model tree with zero event edges collapsed) in Newick format
rose.mt - binary model tree in Newick format
rose.aln.true.fasta - true alignment in FASTA format
rose.mt.internal - binary model tree with all nodes named in Newick format
rose.aln.true.internal.fasta - true alignment for all nodes' sequences in FASTA format

1000 long	1000 medium	1000 short	500 long	500 medium	500 short	100 long	100 medium	100 short
1000L1 1000L2 1000L3 1000L4 1000L5	1000M1 1000M2 1000M3 1000M4 1000M5	1000S1 1000S2 1000S3 1000S4 1000S5	500L1 500L2 500L3 500L4 500L5	500M1 500M2 500M3 500M4 500M5	500S1 500S2 500S3 500S4 500S5	100L1 100L2	100M1 100M2 100M3	100S1 100S2

Biological datasets README

There are 6 biological datasets. Each dataset consists of either DNA or RNA sequences from a variety of markers and taxa.
For each dataset, an associated link to a tarball is listed below. The tarball contains a single directory <dataset name>/R0/ that contains the following files:

cleaned.alignment.fasta - cleaned curated alignment in FASTA format
cleaned.alignment.fasta.name_map - space-delimited two-column data file listing the bijective mapping between taxon names in the cleaned curated alignment file cleaned.alignment.fasta and the original curated alignment file from the Gutell lab CRW

rRNA datasets

23S.M.aa_ag
23S.M
16S.M
16S.M.aa_ag
23S.E
23S.E.aa_ag

For reference purposes, the original Gutell lab CRW datasets can be accessed at the following links. Please note that these original datasets differ from the cleaned datasets above, which were the datasets actually used in the experiments. Furthermore, these original uncleaned curated alignments are not in FASTA format, and are instead in a more verbose GenBank format explained here.

Original uncleaned datasets

23S.M.aa_ag
23S.M
16S.M
16S.M.aa_ag
23S.E
23S.E.aa_ag

Contact

If you have questions or comments, please contact tandy<at>cs<dot>utexas<dot>edu.