From da8ea36c0ffd1a6d99d1a6f39cb80a0576cf52bc Mon Sep 17 00:00:00 2001 From: Todd J Treangen Date: Tue, 24 Mar 2015 03:27:04 -0400 Subject: [PATCH] update docs --- docs/content/parsnp/quickstart.rst | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/content/parsnp/quickstart.rst b/docs/content/parsnp/quickstart.rst index 5b775fe..c2047a4 100644 --- a/docs/content/parsnp/quickstart.rst +++ b/docs/content/parsnp/quickstart.rst @@ -1,6 +1,8 @@ Quickstart ========== +Note: If you are currently using a Parsnp version prior to **v1.2** you should update to use the latest release (currently v1.2). The latest release includes a critical fix for FastTree2; see http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html for further details. + Before you run --------------- @@ -25,14 +27,14 @@ Parsnp is distributed as a precompiled binary that should be devoid of external On OSX: """"""" - 1. wget https://github.com/marbl/parsnp/releases/download/v1.1/parsnp-OSX64-v1.1.tar.gz - 2. tar -xvf parsnp-OSX64-v1.1.tar.gz + 1. wget https://github.com/marbl/parsnp/releases/download/v1.2/parsnp-OSX64-v1.2.tar.gz + 2. tar -xvf parsnp-OSX64-v1.2.tar.gz On Linux: """"""""" - 1. wget https://github.com/marbl/parsnp/releases/download/v1.1/parsnp-Linux64-v1.1.tar.gz - 2. tar -xvf parsnp-Linux64-v1.1.tar.gz + 1. wget https://github.com/marbl/parsnp/releases/download/v1.2/parsnp-Linux64-v1.2.tar.gz + 2. tar -xvf parsnp-Linux64-v1.2.tar.gz Basic usage: """""""""""" @@ -97,10 +99,9 @@ LCB alignment:: -n = : alignment program (default: libMUSCLE) -u = : output unaligned regions? .unaligned (default: NO) -SNP filters:: +Recombination filtration:: - -R = : enable (R)epeat filtering? - -x = : enable recombination filtering? (default: NO) + -x = : enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO) Misc::