1<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> 2<html> 3 <head> 4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> 5 <meta http-equiv="Content-Style-Type" content="text/css"> 6 <title>Software -- Rhodes</title> 7 <meta name="Generator" content="Cocoa HTML Writer"> 8 <meta name="CocoaVersion" content="1348.17"> 9 <style type="text/css"> 10 p.p2 { 11 margin: 0.0px 0.0px 12.0px 0.0px; 12 color: #000000; 13 -webkit-text-stroke: #000000; 14 font-size: 18px; 15 font-family: Times; 16} 17 span.s1 { 18 font-kerning: none; 19 font-size: 24px; 20} 21 span.s2 {font: 18.0px Times; text-decoration: underline ; font-kerning: none; color: #0000ee; -webkit-text-stroke: 0px #0000ee} 22 p.p21 {margin: 0.0px 0.0px 12.0px 0.0px; font: 12.0px Times; color: #000000; -webkit-text-stroke: #000000} 23span.s11 {font-kerning: none} 24span.s21 {font: 12.0px Times; text-decoration: underline ; font-kerning: none; color: #0000ee; -webkit-text-stroke: 0px #0000ee} 25 .red { 26 color: #FF2600; 27} 28 span.s22 {font: 18.0px Times; text-decoration: underline ; font-kerning: none; color: #0000ee; -webkit-text-stroke: 0px #0000ee} 29 span.s23 {font: 18.0px Times; text-decoration: underline ; font-kerning: none; color: #0000ee; -webkit-text-stroke: 0px #0000ee} 30 span.s24 {font: 18.0px Times; text-decoration: underline ; font-kerning: none; color: #0000ee; -webkit-text-stroke: 0px #0000ee} 31 </style> 32 </head> 33 <body> 34 <h2 style="margin: 0.0px 0.0px 14.9px 0.0px; font: 18.0px Times; 35 color: #000000; -webkit-text-stroke: #000000"><span class="s1"><b>Software</b></span></h2> 36 <p class="p2"><strong>MSCsimtester</strong>: An R package for 37 testing simulators of the multispecies coalescent process. </p> 38 <blockquote> 39 <p class="p2">For examples and citation, see "Testing Multispecies 40 Coalescent Simulators using Summary Statistics", E.S. Allman, H. 41 Banos, J.A. Rhodes, 2019</p> 42 <p class="p2"> R package: <a 43 href="software/MSCsimtester_1.0.0.tar.gz"><span class="s2">MSCsimtester_1.0.0.tar.gz</span></a> 44 </p> 45 <p class="p2">Manual: <a href="software/MSCsimtester_1.0.0.pdf"><span 46 class="s2">MSCsimtester_1.0.0.pdf</span></a> </p> 47 <p class="p2"> </p> 48 <p class="p2"> </p> 49 </blockquote> 50 <p class="p2"><strong>MSCquartets</strong>: An R package for 51 analyzing a collection of gene trees under the tree/network 52 multispecies coalescent model through displayed quartets. 53 Version 1.0.5 is now available on CRAN, at <a 54 href="https://cran.r-project.org/web/packages/MSCquartets/"><span class="s22"> 55 https://cran.r-project.org/web/packages/MSCquartets/</span></a></p> 56 <p class="p2">The package 57 includes methods developed in the papers:</p> 58 <blockquote> 59 <p class="p2">[R19] <em>Toplogical metrizations of trees and new 60 quartet methods of tree inference</em>, J.A. Rhodes, IEEE/ACM 61 Trans. Comput. Biol. Bioinf., early access, 2019 62 <a href="https://doi.org/10.1109/TCBB.2019.2917204"><span class="s22"> 63 https://doi.org/10.1109/TCBB.2019.2917204</span></a> 64 </p> 65 <p class="p2">[MAR19] <em>Hypothesis testing near singularities 66 and bondaries</em>, J.D. Mitchell, E.S. Allman, J.A. Rhodes, 67 Electron. J. Statist., 13 (1) 2019 68 <a href="https://projecteuclid.org/euclid.ejs/1561687407"><span class="s22"> 69 https://projecteuclid.org/euclid.ejs/1561687407</span></a> 70 </p> 71 <p class="p2">[YR19] <em>Inferring metric trees from weighted quartets via an intertaxon distance</em>, S. Yourdkhani, J.A. Rhodes, 72 2020 </p> 73 <p class="p2">[ABR19] <em>NANUQ: A method for inferring species 74 networks from gene trees under the coalescent model</em>, E.S. 75 Allman, H. Banos, J.A. Rhodes, Algorithms Mol. Biol., 14 (24) 2019 76 <a href="https://doi.org/10.1186/s13015-019-0159-2"><span class="s22"> 77 https://doi.org/10.1186/s13015-019-0159-2</span></a> 78 </p> 79 <p class="p2"> </p> 80 <p class="p2"> </p> 81 </blockquote> 82 83 <p class="p2"><strong>Scripts for Yourdkhani & Rhodes (2020)</strong>: R scripts and related files 84for the simulation analysis of <em>Inferring metric trees from weighted quartets via an intertaxon distance</em> are
85 available <a href="software/YR2020sims.zip"><span class="s22"> 86 here</span></a>. See comments at beginnings of script files for instructions before running them.</p> 87 <p class="p2"> </p> 88 <p class="p2"> </p> 89 </body> 90</html>
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