Evolutionary genetics software links # softlinks.amnh.org. All Your Base Are Belong To Us. If you don't know what that means, go Wikipedia. AAA Drosophila Genomes wiki. BLAST insect genomes @ NCBI. BLAST eukaryotic genomes @ NCBI. BLAST protozoan genomes @ NCBI. Design by Free CSS Templates.
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Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis | softlinks.amnh.org Reviews
https://softlinks.amnh.org
Evolutionary genetics software links # softlinks.amnh.org. All Your Base Are Belong To Us. If you don't know what that means, go Wikipedia. AAA Drosophila Genomes wiki. BLAST insect genomes @ NCBI. BLAST eukaryotic genomes @ NCBI. BLAST protozoan genomes @ NCBI. Design by Free CSS Templates.
softlinks.amnh.org
Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
http://softlinks.amnh.org/molevol.html
Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined. A program package implementing a variety of sophisticated models of nucleotide and protein sequence evolution via ML. Allows to test alternative hypotheses using likelihood ratio tests. Not recommended for tree-building. Handy for ML and hypothesis testing. Also tests for selection. Customizable through its batch language. Simulates the evolution of nucleotide and aminoacid sequences along a ph...
Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
http://softlinks.amnh.org/alignment.html
Implements a joint Bayesian estimation of alignment and phylogeny. Instead of inferring trees based on a single fixed alignment, it considers near-optimal alignments when estimating the phylogeny. In addition, it can produce alignments colored to indicate uncertain areas of the alignment. Command-line interface. Uses BLAST to align problematic nucleotide sequences. A classic with many Web servers to be searched online. Local and global alignments. To run it locally you must download the source code a...
Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
http://softlinks.amnh.org/popgen.html
A program for Bayesian MCMC analysis of molecular sequences. Orientated towards molecular clock analyses. Not for constructing phylogenies but rather testing evolutionary hypotheses without preconditioning on a single tree topology. Uses MCMC to average over tree space, so that each tree is weighted proportionally to its posterior probability. Implements a Bayesian generalized skyline plot. Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined.
Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
http://softlinks.amnh.org/microsatellites.html
Descriptive statistics, distances, miscellaneous. Rarefaction for allelic richness, private allelic richness, and private allelic richness for combinations of populations. Alleles In Space, TFPGA, Mantel-Struct, AMOVA-PREP. See website for more info. Combines allele data of (partly) overlapping size via ML. Creates and converts input files for 50 programs. Estimates null allele frequencies via a EM algorithm and Fst when null alleles are present via the C2 method. An all-time classic for F-statistics.
Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
http://softlinks.amnh.org/index.html
Evolutionary genetics software links # softlinks.amnh.org. All Your Base Are Belong To Us. If you don't know what that means, go Wikipedia. AAA Drosophila Genomes wiki. BLAST insect genomes @ NCBI. BLAST eukaryotic genomes @ NCBI. BLAST protozoan genomes @ NCBI. Design by Free CSS Templates.
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note2self: November 2007
http://cyclotis.blogspot.com/2007_11_01_archive.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Friday, November 9, 2007. Attack of the flies! The 12 genomes are out! Check out the relevant papers in. Posted by sergios-orestis kolokotronis. Wednesday, November 7, 2007. Elephant on a trampoline. I couldn't resist (doing reseach on elephants and all). a great animation movie! Posted by sergios-orestis kolokotronis. Subscribe to: Posts (Atom). Programs for evolutionary genetics. Inst for Comparative Genomics @ AMNH.
note2self: Debunking junk science
http://cyclotis.blogspot.com/2008/10/debunking-junk-science.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Monday, October 13, 2008. By science writer Michael Shermer. Founder of The Skeptics Society. And editor of Skeptic. Posted by sergios-orestis kolokotronis. Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Programs for evolutionary genetics. Inst for Comparative Genomics @ AMNH. Center for Conservation Genetics @ AMNH. Phylogenomics (J. Eisen). IPhylo (R. Page).
note2self: August 2007
http://cyclotis.blogspot.com/2007_08_01_archive.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Wednesday, August 15, 2007. Nature Editorial: ERC not disclosing the state-members distribution of its grants shortlist. 448, 727-728 (16 August 2007). Division of labour: The European Research Council. Shouldn't be coy about saying who will get its first set of grants. The ERC's mission is perhaps unprecedented in the brief history of the European Union (EU). It has to distribute large amounts of European money &...
note2self: May 2009
http://cyclotis.blogspot.com/2009_05_01_archive.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Thursday, May 21, 2009. Elephant paints autoportrait [ link. Posted by sergios-orestis kolokotronis. Subscribe to: Posts (Atom). Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Programs for evolutionary genetics. Inst for Comparative Genomics @ AMNH. Center for Conservation Genetics @ AMNH. Phylogenomics (J. Eisen). IPhylo (R. Page). New York, NY, United States.
note2self: September 2007
http://cyclotis.blogspot.com/2007_09_01_archive.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Saturday, September 8, 2007. Comes now in a new webserver flavor called RAxML Black Box. This is in addition to the RAxML webserver on the CIPRES Portal. Accepts multiple outgroups (thanx, Alexis :-), does DNA and AA (not combined), accepts partitioned alignment (mixed models), emails a link to the results URL. Brought to you by Alexandros Stamatakis. Posted by sergios-orestis kolokotronis. Subscribe to: Posts (Atom).
note2self: February 2008
http://cyclotis.blogspot.com/2008_02_01_archive.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Monday, February 11, 2008. An inverse relationship between publication output and beer consumption. Grim T. (2008) A possible role of social activity to explain differences in publication output among ecologists. Posted by sergios-orestis kolokotronis. Subscribe to: Posts (Atom). Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Programs for evolutionary genetics.
note2self: An inverse relationship between publication output and beer consumption
http://cyclotis.blogspot.com/2008/02/inverse-relationship-between.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Monday, February 11, 2008. An inverse relationship between publication output and beer consumption. Grim T. (2008) A possible role of social activity to explain differences in publication output among ecologists. Posted by sergios-orestis kolokotronis. Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Programs for evolutionary genetics. Inst for Comparative Genomics @ AMNH.
note2self: Elephant on a trampoline
http://cyclotis.blogspot.com/2007/11/elephant-on-trampoline.html
Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Wednesday, November 7, 2007. Elephant on a trampoline. I couldn't resist (doing reseach on elephants and all). a great animation movie! Posted by sergios-orestis kolokotronis. Notes on evolutionary biology papers/programs and other stuff: a non-frequent approach. Programs for evolutionary genetics. Inst for Comparative Genomics @ AMNH. Center for Conservation Genetics @ AMNH. Phylogenomics (J. Eisen).
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Evolutionary Genetics Software Links by Sergios-Orestis Kolokotronis
Evolutionary genetics software links # softlinks.amnh.org. All Your Base Are Belong To Us. If you don't know what that means, go Wikipedia. AAA Drosophila Genomes wiki. BLAST insect genomes @ NCBI. BLAST eukaryotic genomes @ NCBI. BLAST protozoan genomes @ NCBI. Design by Free CSS Templates.
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