Science for Life Laboratory, Stockholm University, SE-17121, Solna, Sweden.
Bioinformatics. 2012 Nov 15;28(22):2994-5. doi: 10.1093/bioinformatics/bts548. Epub 2012 Sep 14.
PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters.
PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request.
joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se.
PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).
PrIME-DLRS（俗称“Delirious”）是一个系统发育软件工具，可同时推断和协调基因树给定的物种树。它考虑了复制和丢失事件、松弛的分子钟，旨在研究同源基因家族，例如在涉及多个物种的比较基因组学环境中。PrIME-DLRS 使用贝叶斯 MCMC 框架，输入是具有分歧时间和多重序列比对的已知物种树，输出是基因树和模型参数的后验分布。
PrIME-DLRS 在 New BSD License 下可用于 Java SE 6+，JAR 文件和源代码可从 http://code.google.com/p/jprime/ 下载。还有一个稍旧的 C++版本作为 Ubuntu 的二进制包提供，在 http://prime.sbc.su.se 上有下载说明。C++源代码可应要求提供。
joel.sjostrand@scilifelab.se 或 jens.lagergren@scilifelab.se。
PrIME-DLRS 基于可靠的概率模型（Åkerborg 等人，2009 年），并已在合成和生物数据集上进行了彻底验证（在线补充材料）。
