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Center for Comparative Genomics 

July 25, 2012

CCG PhyloCluster updates

July 25, 2012

We have added some new apps to the PhyloCluster and upgraded others:

NEW:

BayesTraits - A program by Mark Pagel that enables the analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.

Structure 2.3.4 - Structure by Pritchard, Stephens and Donnelly can be used for inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

UPDATED:

BEAST updated to 1.7.2 - We have also added the ability to select a random seed for each analysis. This will permit users to run multiple independent analyses of the same input file and combine them as a single large analysis with uniques starting seeds. This is useful if you are not getting acceptable “efeffective sample size” (ESS) values (typically below 100) with single runs and need to run many more generations. For e.g., if a 50 million generation run is not producing acceptable ESS values you could run 8 simultaneous 50 million generation analyses and combine them for a total of 400 million generations. Having a unique starting seed improves independence. We have kept BEAST 1.6.2 in case you still have xml files generated by BEAUTi 1.6.2.

MrBayes updates to 3.2.1 - For more info about the Mrbayes update, please visit the Mrbayes website.

RAxML updated to 7.2.6 - We have added the ability to use constraint and backbone trees in your Likelihood analyses. The trees must be in Newick (phylip) format. standard NEXUS trees can be converted in TreeView or Mesquite and the taxon names MUST be identical to those in you input file. Please visit the RAxML manual for details.




Filed under: CCG Laboratory — brian @ 1:37 pm

March 23, 2012

Welcome to the new CCG blog

This new blog for the California Academy of Sciences’ Center for Comparative Genomics (CCG) is intended to keep its users and friends up to date on the latest CCG news, events and expeditions.


Filed under: CCG Laboratory,Expeditions — brian @ 11:14 am

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