The Exelixis Lab

Enabling Research in Evolutionary Biology

ForeSeqs: Prediction of missing sequences and branch lengths


ForeSeqs is a tool for predicting sequences and branch lengths in data sets with whole missing partitions. Missing data usually lead to wrong phylogenetic inferences, since branches leading to unexistent taxa can have arbitrary lengths. Terraces in the phylogenetic tree space is another problem derived from missing taxa. Even though this problem can be avoided by linking branch lengths across partitions, the missing data can affect the phylogenetic inferences.


Get the most up-to-date ForeSeqs version from github.


Please refer to the source code repository for usage instructions.

User Support

Please send all your questions and feature requests regarding ForeSeqs to the RAxML google group.


Darriba, D., WeiƟ, M., & Stamatakis, A. (2016). Prediction of Missing Sequences and Branch Lengths in Phylogenomic Data. Bioinformatics, btv768. advance online access