Gouy Manolo, Tannier Eric, Comte Nicolas, Parsons David P
Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France.
INRIA Grenoble-Rhône-Alpes, Montbonnot, France.
Methods Mol Biol. 2021;2231:241-260. doi: 10.1007/978-1-0716-1036-7_15.
We present Seaview version 5, a multiplatform program to perform multiple alignment and phylogenetic tree building from molecular sequence data. Seaview provides network access to sequence databases, alignment with arbitrary algorithm, parsimony, distance and maximum likelihood tree building with PhyML, and display, printing, and copy-to-clipboard or to SVG files of rooted or unrooted, binary or multifurcating phylogenetic trees. While Seaview is primarily a program providing a graphical user interface to guide the user into performing desired analyses, Seaview possesses also a command-line mode adequate for user-provided scripts. Seaview version 5 introduces the ability to reconcile a gene tree with a reference species tree and use this reconciliation to root and rearrange the gene tree. Seaview is freely available at http://doua.prabi.fr/software/seaview .
我们展示了Seaview 5版本，这是一个多平台程序，用于根据分子序列数据进行多序列比对和系统发育树构建。Seaview提供对序列数据库的网络访问、使用任意算法进行比对、简约法、距离法以及使用PhyML构建最大似然树，还能显示、打印、复制到剪贴板或生成本地有根或无根、二叉或多叉系统发育树的SVG文件。虽然Seaview主要是一个提供图形用户界面以指导用户进行所需分析的程序，但它也拥有适合用户提供脚本的命令行模式。Seaview 5版本引入了将基因树与参考物种树进行比对并利用这种比对来确定基因树根的位置和重新排列基因树的功能。可从http://doua.prabi.fr/software/seaview免费获取Seaview。
