Treeness Triangle

Spectronet 1.27

Min-Max Squeeze

This program implements the methods described in

Holland, B. R., K.T. Huber, D. Penny, and V. Moulton. 2005. The MinMax Squeeze: Guaranteeing a minimal tree for
population data. Mol. Biol. Evol. 22:235-242.

and

Pierson, M.J., R. Martinez-Arias, B.R. Holland, N.J. Gemmell, M.E. Hurles, and D. Penny. 2006. Deciphering Past
Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes. Mol. Biol. Evol. 23(10).

for finding lower bounds on the parsimony score of an alignment.

Two-States Triplet Markov — 2STM

2STM calculates Markov matrices from 2-state character data sets with 3 sequences simultaneously. The program reads 4-state character nucleotide data sets and outputs estimates of the three Markov matrices from the root to each taxon. 2STM also calculates the variability of estimates (bootstrap) and some simple statistics, such as composition of nucleotide characters, either in 4 states or 2 states.

Contact Details

Michael Woodhams
Allan Wilson Centre
Institute of Molecular
BioSciences PN462
Massey University
Palmerston North,
New Zealand
Phone: +64 6 356 9099
ext 2570
E-mail
m.d.woodhams@massey.ac.nz

Site Strip Search — For site-stripping analyses of nucleotide alignments.

This script selects subsets of taxa from a given alignment. The subsets are chosen arcording to the homoplasy of the sites. The resulting data set may be automatically sent to PAUP* or MrBayes for further analysis.

This beta version has been tested on Linux and Windows operating systems.

Contact Details

Warwick Allen
Allan Wilson Centre
Institute of Molecular
BioSciences PN462
Massey University
Palmerston North,
New Zealand
Phone: +64 6 356 9099
ext 5449
E-mail
w.p.allen@massey.ac.nz

Quartet-Imputation Supernetworks

This program implements the methods described in

Holland, B. R., G. Conner, K. Huber, V. Moulton. 2006. Imputing supertrees and supernetworks from quartets. Systematic Biology (to appear).

and

Holland, B. R., G. Conner, K. T. Huber, V. Moulton. 2006. Imputing supertrees and supernetworks from quartets, (1 page abstract). In: 6th Workshop on Algorithms in Bioinformatics (WABI 2006) Eds B. Moret and P. Buchner, Lecture Notes in Bioinformatics. 4175:162.

Contact Details

Barbara Holland
Allan Wilson Centre
Institute of Molecular
BioSciences PN462
Massey University
Palmerston North,
New Zealand
Phone: +64 6 356 9099
ext 7939
E-mail
b.r.holland@massey.ac.nz

Genotyping Utilities Package

GenoTyper Rearranger (GTR) is a utility that converts the output AFLP data from genotyping programs (currently ABI's Gene­Mapper and Soft­Genetics' Gene­Marker) to various formats, allowing easier display and mani­pulation.

AFLP Replicate Difference Calculator is a utility calculates the difference of some parameter (peak height, for example) between replicates in a table of AFLP data. This script takes two inputs: the AFLP data and a table that declares which samples are replicates of which other samples.

See the AFLP page for more details.

Contact Details

Warwick Allen
Allan Wilson Centre
Institute of Molecular
BioSciences PN462
Massey University
Palmerston North,
New Zealand
Phone: +64 6 356 9099
ext 5449
E-mail
w.p.allen@massey.ac.nz

LineageSpecificSeqgen is an extension to the seq-gen program that allows generation of sequences with both changes in the proportion of variable sites and changes in the rate at which sites switch between being variable and invariable.

Ref: Shavit L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evolutionary Biology 2008 (in press).