From 4d4223562bfeb7d8aba7115b9a03c7f0d490910c Mon Sep 17 00:00:00 2001 From: "B. Watson" Date: Sat, 12 Mar 2022 14:40:15 -0500 Subject: [PATCH] academic/treebest-ensembl: Wrap README at 72 columns. Signed-off-by: B. Watson --- academic/treebest-ensembl/README | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/academic/treebest-ensembl/README b/academic/treebest-ensembl/README index b6639d304d..f91a651be9 100644 --- a/academic/treebest-ensembl/README +++ b/academic/treebest-ensembl/README @@ -10,16 +10,18 @@ TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group. -This is the Ensembl Compara modifications version. The main new features -are: +This is the Ensembl Compara modifications version. The main new +features are: 1) -s option in treebest sdi, to allow a user-defined species tree. T node-tag in the NHX output: a bit-field listing the input trees 2) that support the node. 3) -I option in treebest nj, to carry on the T tags from the input tree -4) -Z option in treebest best, to redefine the PhyML variable MIN_DIFF_LK -5) -X option in treebest best, to give a higher weight to the likelihood - that comes from the reconciliation with the species tree (default 1) +4) -Z option in treebest best, to redefine the PhyML variable + MIN_DIFF_LK +5) -X option in treebest best, to give a higher weight to the + likelihood that comes from the reconciliation with the species tree + (default 1) 6) -I option in treebest best, to start from the input tree instead of building one 7) Species-intersection scores are now also reported as floating-point