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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.

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

Download IsoSel

Single thread compilation
Compilation in HPC
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source code

See the compilation section for more information.

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

Typical Use

Available options

<infile> Multiple sequences input file in fasta format.
-f Tab delimited file with sequence names and corresponding coding gene identifier.
-a Alignment algorithm. Must be muscle, clustalo or mafft (default: muscle).
-b Number of bootstrap replicates. Must be a positive integer (default: 30).
-t Number of threads. Must be a positive integer (default: 1).
-m Substitution model for distance matrices computation. Must be: Blo, JTT, JTTfast, Kim, LG, Obs, PAM, Pois or WAG (default: LG).
-e Missing distances estimation method. Must be none, MinMax or additive (default: additive).
-s Number used as seed for bootstrap replicates (default: 0) .
-gap Option to penalize isoforms introducing gaps in alignment (default: off).
-short Option to penalize isoforms well aligned but too short (default: off).
-DS Option to use the mean of distances as scores (default: off).
-WOT Option to compute scores with all input dataset sequences when the option -DS is used (default: off).
-auto Option to automatically select the best option among -DS, -gap, -short or default parameters (default: off).
-quiet Do not report progress (default: off).
-outdir Path to the directory results (default: directory of the input file)
-n Output name (default: output)


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

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.


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


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.