TREEFINDER computes phylogenetic trees from molecular sequences.

License change and re-release in October 2015:

Starting from 1st October 2015, I do no longer permit the usage of my TREEFINDER software in the following EU countries: Germany, Austria, France, Netherlands, Belgium, Great Britain, Sweden, Denmark. For all other countries, the old license agreement remains valid. USA has already been excluded from using Treefinder in February 2015. This is all in accordance with the license agreement stated in the TREEFINDER manual since the earliest versions, which reserves me the right to change the license agreement at any time. I can do this because Treefinder is my own property.

The TREEFINDER version of March 2011 together with the above and all previous license changes becomes "the latest version" according to license statement in the manual!

License change and re-release in February 2015:

Starting from 1st February 2015, I do no longer permit the usage of my TREEFINDER software in the USA.

New features in March 2011:

• support for multicore processors
• parallel bootstrapping
• parallel model selection
• TL extended for parallel programming
• more protein models: FLU, mtZOA, EX.., EHO.., EXEHO..
• convenient installer for Windows

New features in October 2008:

• minor bugfix (November 10)
• generalized partition model, which
• includes both proportional and separate model
• resampling of calibration times
• improved TL manual

New features in June 2008:

• MAP crash repaired (June 16)
• user-definable substitution model: MAP
• computation of sitewise rates
• automatic generation of data partitions

New features in April 2008:

• mixed protein model: MIX
• Dayhoff groups protein model: DG
• improved model proposer

The Tree Viewer

New features in March 2008:

• bugfix and LG protein model (April 7)
• computation of pairwise ML distances
• construction of distance trees: NJ, BIONJ
• least squares fitting of edge lengths
• more DNA models: J1, J2, J3 (= TIM), TVM
• more protein models: betHIV and witHIV
• improved model proposer
• more efficient TL

New features in January 2008:

• more bugfixes (January 28, March 7)
• model proposer for DNA, Proteins, RNA
• sequence simulation dialog
• improved tree search algorithm
• several bugfixes

New features in November 2007:

• improved tree search algorithm
• tree formats extended for edge length intervals
• consensus trees with edge length intervals
• easier divergence time intervals

New features in June 2007:

• general model selection and testing, using
• paired sites tests with information criterion
• parametric bootstrap test with information criterion
• output of sitewise information criteria
• experimental simulated information criterion of my own: SimIC
• one more cost function for rate smoothing: NPRS-LOG

New features in May 2007:

• more paired-sites tests: ELW, BP, KH, SH, WSH, AU
• LRSH edge support replaced by LR-ELW (based on expected-likelihood weights)
• output of sitewise likelihoods
• information criteria: AIC, AICc, BIC
• protein models with optimized and empirical amino acid frequencies (+F)
• utilities to concatenate alignments, reports and sample files
• utilities to change tree topology and arrange hypotheses
• parallel bootstrapping
• Intel and G5 binaries for the Mac

New features in February 2007:

• parametric bootstrapping from a dialog
• simulation of partitioned sequences
• sequence simulation along reports
• mtArt protein model

New features in May 2006:

• global search from multiple start trees
• user-definable start trees
• start tree generator
• export of tip distances
• bootstrap analysis under topological constraints
• confidence limits for all numerical results, including
• confidence limits for divergence times
• simplified tree calibration
• minor bugfixes

New features in October 2005:

• empirical rRNA models with secondary structure
• PMB protein model
• SH test for user-supplied topologies
• faster computation of edge support
• improved manual

New features in June 2005:

• another bug repaired (July 4)
• protein models BLOSUM, cpREV, Dayhoff, JTT, mtMam, mtREV, rtREV, VT, WAG, GTR20
• 2-state and 3-state models for DNA/RNA
• SH-based approximate bootstrapping (LRSH-RELL)
• data partitioning with separate rates, compositions, models, heterogeneity
• extended and filter-based manipulation of sequence data
• no more chi-square test for compositional equilibrium
• bugfixes

New features in December 2004:

• frontend bug fixed
• improved Macintosh installation (January 9)

New features in November 2004:

• new and faster tree search algorithm
• new tree calibration methods GRMD and LRMD
• multiple calibration points and intervals
• utility to visualize compositional equilibrium
• no more optimization under molecular clock

New features in June 2004:

• some minor completions

New features in April 2004:

• revised frontend
• Solaris version

New features in March 2004:

• edge length optimization under molecular clock
• fast approximate bootstrapping (LRP)
• midpoint tree rooting utility
• codon position filter

New features in December 2003:

• rate profiling along sequence alignments
• non-parametric rate smoothing (NPRS)
• more informative TL manual

New features in October 2003:

• dozens of new TL functions
• dialog for bootstrap analysis
• topology counter
• improved tree viewer and rerooter
• test for compositional equilibrium
• mutation profile utility

New features in March 2003:

• model refinement for protein coding sequences
• estimation of codon position rates
• bootstrap analysis
• stop button
• minor bugfixes
• extended documentation
• improved tree import and export
• new consensus routine producing edge lengths

New features in November 2002:

• tree search under topological constraints
• extended documentation and bugfixes
• missing tree export menu included
• improved graphical frontend
• NEXUS format supported

New features in September 2002:

• first public release
• comparison with other phylogeny programs
• fastest maximum likelihood phylogeny program on PC