Difference between revisions of "Bio-ind-study"
(Bioinformatics Independent Study) |
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| − | Analyzing different approaches to generating parsimonious phylogenetic trees across turtle taxa. | + | <h2>Analyzing different approaches to generating parsimonious phylogenetic trees across turtle taxa.</h2> |
| + | <p>The goal of this project is to analyze several different approaches to generating parsimonious phylogenetic trees across turtle taxa. During the course of this project, I will use and evaluate several bioinformatics tools for generating phylogenetic trees including PAUP, maximum likelihood, maximum parsimony, gene trees and amino acid analysis. I will attempt to answer such questions as why do these different methods produce different trees, what gene, trait or character is the most important or heavily weighted and any other questions generated by my research.</p> | ||
| + | |||
| + | PAUP - tools for inferring and interpreting phylogenetic trees, http://paup.csit.fsu.edu | ||
| + | * [[paup-software|Running the software]] | ||
| + | * [[paup-science|The science]] | ||
| + | |||
| + | MrBayes - Bayesian estimation of phylogeny, http://mrbayes.csit.fsu.edu | ||
| + | * [[mrbayes-software|Running the software]] | ||
| + | * [[mrbayes-science|The science]] | ||
| + | |||
| + | Post-run analysis using MB | ||
| + | * sump filename=Testudinoidea_all-1.nex.mb nruns=1 | ||
| + | * sumt filename=Testudinoidea_all-1.nex.mb.t nruns=1 ntrees=1 burnin=300 (after reloading .mb file with commented-out execution statements) | ||
| + | * Output from sump - [[mb-sump-output]] | ||
| + | * Output from sumt - [[mb-sumt-output]] | ||
| + | |||
| + | Google Docs pointer | ||
Latest revision as of 13:02, 28 April 2008
Analyzing different approaches to generating parsimonious phylogenetic trees across turtle taxa.
The goal of this project is to analyze several different approaches to generating parsimonious phylogenetic trees across turtle taxa. During the course of this project, I will use and evaluate several bioinformatics tools for generating phylogenetic trees including PAUP, maximum likelihood, maximum parsimony, gene trees and amino acid analysis. I will attempt to answer such questions as why do these different methods produce different trees, what gene, trait or character is the most important or heavily weighted and any other questions generated by my research.
PAUP - tools for inferring and interpreting phylogenetic trees, http://paup.csit.fsu.edu
MrBayes - Bayesian estimation of phylogeny, http://mrbayes.csit.fsu.edu
Post-run analysis using MB
- sump filename=Testudinoidea_all-1.nex.mb nruns=1
- sumt filename=Testudinoidea_all-1.nex.mb.t nruns=1 ntrees=1 burnin=300 (after reloading .mb file with commented-out execution statements)
- Output from sump - mb-sump-output
- Output from sumt - mb-sumt-output
Google Docs pointer
