Mesa Macro-evolutionary analysis and simulation package
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analyze simulate evolution evolution analysis simulate evolution evoultion simulation

Mesa Description

Macro-evolutionary analysis and simulation package Phylogenies are smoking guns. An evolutionary history carrys in its very shape the fingerprints of every process that effected its creation: extinctions, key adaptations, radiations, colonizations, changes in the tempo and mode of macroevolution. Unfortunately analysing phylogenies is difficult. The calculations of interest to any investigator are sometimes intricate and labour-intensive. They are also often across several programs, if there is a software implementation at all. The statistical significance of results often require the comparison of hundreds to thousands of trees. Finally, metrics may be fragile to the mode of evolution a phylogeny grew under. The result of these problems is that phylogenetic analysis is often hard work, and it is difficult to know what to make of the answers. MeSA is an software application created to alleviate these problems. Although MeSA really only does four things, the big win for its users is that all these are in one software package and can be used in conjunction with each other, and semi-automated.Thus, the problems of transferring data between programs and possible corruption or misintepretation of results are avoided.NOTE: MeSA is unrelated to the graphics library, spreadsheet, airline, academic association, college,search engine, engineering society, town or topographical feature of the same name. Here are some key features of "MeSA": Manipulations: · MeSA allows datasets to be manipulated in sophisticated ways. Phylogenetic trees and life history traits can be edited, duplicated or deleted. Branchlengths can be systematically modified, taxa deleted according to complex conditions, traits modified globally and selectively. The entire dataset can also be backed up and restored at any moment. Analysis: · MeSA incorporates a large number of calculations that can analyse diversity within a phylogeny (e.g. phylogenetic diversity), diversity across communities (e.g. Shannon-Weiner index), measures of macroevolutionary process (e.g. Fusco-Cronk imbalance), and gather information selectively across taxa. Simulations: · MeSA allows phylogenies to be grown under sophisticated scenarios where speciation and extinction rates can be effected by the traits of the taxa involved or global attributes of the phylogeny. Simulations can be further adorned by mass extinctions and the evolution of life history traits. Automation: · In order to allow the production and testing of a large number of phylogenies, MeSA lets users construct chains of actions (manipulations, analyses and simulations) that may be run as a single unit, looping over groups of commands, saving and restoring data. Thus one may easily generate test a large number of replicates for statistical validity. What's New in This Release: · For obscure technical reasons (line-endings and reading modes), the PC version of MeSA would refuse to read some files that were read fine on the Mac. It now seems to be fixed. Thanks to Henri for identifying this problem.

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