Missing data prediction software tools | Phylogenomics
The presence of missing data in large-scale phylogenomic datasets has negative effects on the phylogenetic inference process. One effect that is caused by alignments with missing per-gene or per-partition sequences is that the inferred phylogenies may exhibit extremely long branch lengths.
Visualizes phylogenetic relationships and metadata for Pezizomycotina, downloads alignments for six loci and performs placement of unknowns using either BLAST or phylogeny-based approaches in RAxML. T-BAS has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades; (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments; (iii) User-customizable metadata can be visualized on the tree.
Provides a method of combining any number of empirical observations (even incomplete) with the phylogenetic tree to obtain a complete set of estimates for missing parameter values. PhyloPars performs real-time cross-validation and provides further insight in the accuracy and bias expected for estimated values. The server allows for easy, efficient estimation of metabolic parameters, which can benefit a wide range of fields including systems biology and ecology.
Algorithms for correcting excessively long branch lengths induced by missing data and methods for predicting/imputing missing sequence data. ForeSeqs was evaluated by systematically removing sequence data from three empirical and 100 simulated alignments.
Allows to determine reconciliation feasibility. PLCT aims to encode the set of species-specific loci that must be orthologous. It captures the constraints implied by the multiple loci and multiple samples. The tool complements existing bootstrap methods for measuring gene tree quality. It can definitively identify when a gene tree topology has been affected by reconstruction error or gene conversion.