IsoSel

IsoSel (Isoform Selector) is designed for selecting alternative isoforms in the context of phylogenetic reconstructions. Based on bootstrapped trees and perturbed alignments, IsoSel assigns alignment scores to input sequences. Optionally, the user can provide a file in which the information on isoform locus tag is given. In this case, IsoSel will also create a file in Fasta format containing the filtered dataset (i.e. in which only the best isoform per gene is kept).

IsoSel was developped by Héloïse Philippon, Alexia Souvane, Céline Brochier-Armanet and Guy Perrière

Use of IsoSel

IsoSel is a command line software.

./run_isosel <infile> [-f <isoforms_locus_tag_file>] [-a <alignment_algorithm>] [-b <number_of_bootstrap>]

[-t <threads_number>] [-m <substitution_model>] [-e <missing_distance_estimation_method>]

[-n <output_name>] [-outdir <output_directory>] [-s <seed_number>] [-gap] [-short]

[-DS] [-WOT] [-auto] [-quiet]

See Typical Use section for more explanations or the README file.

Download IsoSel

If you encounter some problems when using IsoSel, please contact Guy Perrière. Any comments or suggestions are welcome.

Typical Use

• Example data: You will find an example file in the program distribution (data directory) or here.
  The example.fasta file is a dataset of 59 amino acid sequences from different Metazoan organisms.
  You will also find the 200 datasets used for the IsoSel article here.

• Basic usage:

  ./run_isosel example.fasta
  

  By default, without the "-outdir" option, the results will be written in the directory of the input file.
  Three output files will be created:

  - output.aln : the alignement generated by the chosen alignment program.
  - output.log : the log file.
  - output.scores : the file with all sequences scores.

• With transcript information:

  ./run_isosel example.fasta -f isoforms_locus_tag.txt
  

  By default, without the "-outdir" option, the results will be written in the directory of the input file.
  Four output files will be created:

  - output.aln : the alignement generated by the chosen alignment program.
  - output.log : the log file.
  - output.scores : the file with all sequences scores.
  - output_filtered.fasta : the dataset filtered in fasta format.

Available options

Compilation

IsoSel needs the gcc compiler v. 4.9 minimum (on Linux : apt-get install gcc-4.9).

• Installation as root in /usr/local/bin/:

  $ tar -xzf IsoSel.tar.gz
  $ cd IsoSel
  $ cd src
  $ make all
  $ sudo make install

• Installation in a particular path /MyPathToIsoSel/bin:

  $ tar -xzf IsoSel.tar.gz
  $ cd IsoSel
  $ cd src
  $ make all
  $ make install DESTDIR=/MyPathToIsoSel/bin/

• Then, you must fix the "ISOSEL_BIN" variable to "MyPathToIsoSel/bin/" in the /bin/run_IsoSel file.

IsoSel needs also muscle v3.8 , mafft v7.266, clustalo v1.2.0 and seaview v4.4.1 which are provided in the bin/ directory of the source code, with the permission of the authors.

Reference

If you use IsoSel in a published work, please cite the following reference:

Philippon H., Souvane A., Brochier-Armanet C. and Perrière, G. (2017) IsoSel: Protein Isoform Selector for Phylogenetic Reconstructions. PLoS One 12(3):e0174250. Online version

Licensing

IsoSel is distributed according to the CeCill Licence which is a GNU/GPL .

All binaries are integrated in the IsoSel distribution with the permission of the authors.