PhyloSofS perform the phylogenetic reconstruction for the transcripts, but it can take several hours.

ThorAxe Orthology detection between exons and Evolutionary Splicing Graph construction
PhyloSofS Transcripts' phylogenies reconstruction

Ensembl data
Orthology relationship to use: 1:1, 1:n or m:n. It is possible to get more genes and transcripts by allowing for 1:n or m:n orthologs. However, ThorAxe can not ensure that the s-exons contain only orthologous exonic regions under that setup.
Exons shorter than this value will not be considered in the clustering step.
Pairwise alignment
Minimum required coverage for the shortest exon in the pair.
Penalty for a gap opening.
Penalty for gap extensions.
Multiple Sequence Alignment
Length of padding (symbol X) separating sub-exons that never co-occur in a transcript.
Try and re-assign the sub-exons that do not align against any other sequence in the MSA to another cluster (disabled by default).
Turn off the refinement of s-exons through shifting of the very small sequence stretches isolated by gaps (enabled by default).
Turn off the refinement of s-exons through disintegration of the 1-column s-exons (enabled by default).
Alternative splicing event detection
Minimum number of supporting species required for a path to be considered.
Minimum number of supporting transcripts required for a path to be considered.
List of transcript features (column names in the path_table) separated by commas or line returns used to sort the transcripts (rows in the path_table).
Number of phylogenetic forest structures sampled and evaluated by the algorithm.
Turn off the removal of s-exons that appear in only one transcript (enabled by default).
Optional. We will e-mail you when the computation is done. Note that depending on the demand, the calculation may take more than an hour to complete.