Analysis settings

Several analysis-related settings are available for customization by selecting Analysis | Settings from the menu bar. This brings up the Analysis Settings dialog, which contains tabs for three groups of settings.

Application settings

• Path to Bambe - location on disk where the Bambe executable can be found.
• Path to Barce - location on disk where the Barce executable can be found.
• Path to Fitch - location on disk where the Fitch executable can be found.
• Scratch directory - location on disk to store temporary files.

The Bambe, Barce, and Fitch executables are required for running PDM, HMM, and DSS analysis methods respectively. Under Microsoft Windows systems, these files are pre-compiled and included as part of TOPALi, and will be linked to automatically the first time the application is run. Under other systems (Unix/Linux), these files must be compiled externally, before being linked to from within TOPALi.

Tree generation settings

Three tree generation methods are available, ranging from least accurate (but fast), to most accurate (but slower).

• Jukes Cantor + Uniform Rates Model/Neighbor Joining - uses the Jukes Cantor model of nucleotide substitution to estimate pairwise distances. The tree is then estimated using the Neighbor Joining method.
• F84 + Gamma Rates Model/Neighbor Joining - uses the Felsenstein 84 nucleotide substitution model plus Gamma Rates heterogeneity model to estimate pairwise distances. The tree is then estimated using the Neighbor Joining method.
• F84 + Gamma Rates Model/Bayesian Phylogenetic Analysis - uses the Felsenstein 84 nucleotide substitution model plus Gamma Rates heterogeneity model. The tree is estimated directly from the alignment data using the Bayesian (MCMC) Phylogenetic approach (via Bambe).

The Force all negative branch lengths to be zero option ensures that no trees can be created that have negative branch lengths. When selected, any trees with negative branches will automatically have those branches set to a length of zero instead.

Auto-Partitioning settings

• Discard partitions less than X nucleotides in length - specifies the minimum size a partition must be to be included in a partition list.

Note that this option affects the auto-partition option available by selecting Analysis | Auto-Partition Alignment, in addition to defining the setting used when a report auto-partitions an alignment for tree selection.