:: DESCRIPTION
JaDis is a program for computing distances between nucleic acid sequences. It allows specific comparison of coding sequences, of non-coding sequences, or of coding and non-coding sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Goncalves I, Robinson M, Perriere G, Mouchiroud D.
JaDis: computing distances between nucleic acid sequences.
Bioinformatics. 1999 May;15(5):424-5.
:: DESCRIPTION
Distory is a software for geodesic distance between phylogenetic trees and associated functions
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees
John Chakerian, Susan Holmes (2010)
:: DESCRIPTION
rSPR (rooted subtree-prune-and-regraft) is a software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Whidden, C., Beiko, R.G., Zeh, N.
Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments.
In: Proceedings of the 9th International Symposium on Experimental Algorithms, SEA 2010. Lecture Notes in Computer Science, vol. 6049, pp. 141–153. Springer-Verlag (2010)
:: DESCRIPTION
PAUL (Protein Alignment Using Lagrangian relaxation) is a tool for the computation of protein structure alignments based on sparse protein distance matrices
::DEVELOPER
Life Sciences Group, Centrum Wiskunde & Informatica
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Sep 15;26(18):2273-80. doi: 10.1093/bioinformatics/btq420. Epub 2010 Jul 17.
Towards optimal alignment of protein structure distance matrices.
Wohlers I1, Domingues FS, Klau GW.
:: DESCRIPTION
FRETsg is a tool for a fast qualitative analysis of multiple FRET (fluorescence resonance energy transfer) experiments. FRET experiments principally yield the distances between fluorescent dyes, which are commonly used for labelling proteins, DNA, RNA, etc. If multiple FRET experiments are done, it is possible to build a 3D model of the labelled positions. FRETsg finds all positions which obey the measured FRET distances and writes the model to a PDB-type file, which can be easily overlayed with other PDB structures.
::DEVELOPER
Gunnar Schröder and Helmut Grubmüller
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Schroeder, G., & Grubmueller, H. (2004).
FRETsg: Biomolecular structure model building from multiple FRET experiments.
Computer Physics Communications, 158(3), 150-157.
:: DESCRIPTION
IRILmap (Intermated recombinant inbred lines Map) was developed to compute “actual” centiMorgan distances from MapMaker output files (result of “Map” command obtained with the “photo” command) obtained from IRIL data with “RI self” or “RI sib” options (see “Distance calculation” section for details). It is also possible to use IRILmap to convert Haldane distances into Kosambi’s, or reciprocally. Mapping data produced with other software than MapMaker can be used, provided that file formats are respected (see “Format specifications” section for details) and that distances were computed as for RILs by using Haldane & Waddington’s formula. For this purpose, tabulated files are also accepted in addition to MapMaker output files.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Falque M.
IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains.
Bioinformatics. (2005) Aug 15;21(16):3441-2
:: DESCRIPTION
BIONJ is well suited for distances estimated from DNA or protein sequences. BIONJ has better topological accuracy than NJ in all evolutionary conditions; its superiority becomes important when the substitution rates are high and varying among lineages. However, BIONJ and NJ trees are often close or identical, notably when the number of taxa is low. BIONJ retains the speed of NJ and can be applied to very large data sets (> 1000 taxa). BIONJ can be run on several matrices to build bootstrap trees. As usual, distances should be corrected, e.g. using DNADIST or PROTDIST from PHYLIP.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gascuel O.
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
Molecular Biology and Evolution. 1997 14:685-695.
:: DESCRIPTION
MTDIS (mitochondrial DNA distance analysis program) was initially written to calculate genetic distances between populations for restriction site data obtained from single copy DNA sequences (eg. mtDNA). The present version of MTDIS will also calculate inter-population genetic distances for DNA sequence data obtained from single copy DNA.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Danzmann, R.G. 1998.
MTDIS: A computer program to estimate genetic distances among populations based upon variation in single copy DNA.
J. Hered. 89: 283-284.
:: DESCRIPTION
Distance is a program written by Lars Arvestad that implements a least-squares method for estimating general reversible DNA substitution matrices and evolutionary distances.
::DEVELOPER
William J. Bruno and Lars Arvestad
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Mol Evol. 1997 Dec;45(6):696-703.
Estimation of reversible substitution matrices from multiple pairs of sequences.
Arvestad L, Bruno WJ.
:: DESCRIPTION
DISTANCE uses an evolutionary algorithm to find suitable placings on a 2-dimensional surface. Genetic distances between populations (or between individuals) are supplied in your text file.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kinghorn, B.P. and Shepherd, R.K. 2001.
A graphic display of genetic distances between populations.
Assoc. Advmt. Anim. Breed. Genet. 14: 273-276.
