From 4f3e7032ccf07f5afc0919d07ca6b098ce4bf394 Mon Sep 17 00:00:00 2001 From: Ben Fulton Date: Thu, 7 Mar 2019 09:41:35 -0500 Subject: [PATCH] Doc updates --- CHANGELOG.md | 6 ++++++ Makefile.in | 2 +- README.md | 12 ++++++++---- 3 files changed, 15 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 00c4aec..6e42644 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](http://semver.org/). +## [4.2.1] - 2019-03-15 +### Changed +- Fixed a memory leak in situations where branch lengths were almost identical to each other +- Improved error messages when there is an error in the family file +- Fixed bug where the tree was printed twice in the report + ## [4.2] - 2018-07-01 ### Added - tree: a -i parameter is now supported to load a tree from a file. diff --git a/Makefile.in b/Makefile.in index 2e16dad..95d07af 100644 --- a/Makefile.in +++ b/Makefile.in @@ -128,6 +128,6 @@ install: $(RELEXE) .PHONY dist: dist: $(AUX) - mkdir distro + mkdir -p distro tar --transform "s,^,CAFE/," -cf distro/CAFE-@PACKAGE_VERSION@.tar.gz cafe docs example libcommon libtree tests main.cpp $(AUX) diff --git a/README.md b/README.md index 940fe2e..dfc14d8 100644 --- a/README.md +++ b/README.md @@ -9,18 +9,22 @@ gain and loss across a user-specified phylogenetic tree. The distribution of fam sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa. -CAFE v4.2 is the latest in a regular series of releases to the CAFE application. The +[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) + +[![Build Status](https://travis-ci.org/hahnlab/CAFE.svg?branch=master)](https://travis-ci.org/hahnlab/CAFE) + +CAFE v4.2.1 is the latest in a regular series of releases to the CAFE application. The manual and various tutorials may be viewed on the website (https://hahnlab.github.io/CAFE/) . This document describes how to -download and use CAFE v4.2. +download and use CAFE v4.2.1. # Use -The necessary inputs for CAFE v4.2 are: +The necessary inputs for CAFE v4.2.1 are: 1. a data file containing gene family sizes for the taxa included in the phylogenetic tree 2. a Newick formatted phylogenetic tree, including branch lengths -From the inputs above, CAFE v4.2 will compute: +From the inputs above, CAFE v4.2.1 will compute: 1. the maximum likelihood value of the birth & death parameter, λ (or of separate birth and death parameters (λ and μ, respectively), over the whole tree or for user-specified subsets of branches in the tree