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hyginn 2017-11-23 07:19:31 -05:00
parent 75c6efe4a6
commit 359434d863
1 changed files with 8 additions and 8 deletions
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BIN-PHYLO-Tree_building.R
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@ -27,7 +27,7 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> -------------------------------------------------------
#TOC> 1 Calculating Trees 43
@ -36,8 +36,8 @@
#TOC> 1.1.2 ... on Windows 80
#TOC> 1.1.3 ... on Linux 94
#TOC> 1.1.4 Confirming PROMLPATH 99
#TOC> 1.2 Building a maxiiimum likelihood tree 108
#TOC>
#TOC> 1.2 Building a maximum likelihood tree 108
#TOC>
#TOC> ==========================================================================
@ -67,7 +67,7 @@ if (!require(Rphylip, quietly=TRUE)) {
# on your computer Phylip has been installed and define the path
# to the proml program that calculates a maximum-likelihood tree.
# === 1.1.1 ... on the Mac
# === 1.1.1 ... on the Mac
# On the Mac, the standard installation places a phylip folder
# in the /Applications directory. That folder contains all the
# individual phylip programs as <name>.app files. These are not
@ -78,7 +78,7 @@ if (!require(Rphylip, quietly=TRUE)) {
# directly to that subdirectory to find the program it needs:
# PROMLPATH <- "/Applications/phylip-3.695/exe/proml.app/Contents/MacOS"
# === 1.1.2 ... on Windows
# === 1.1.2 ... on Windows
# On Windows you need to know where the rograms have been installed, and you
# need to specify a path that is correct for the Windows OS. Find the folder
# that is named "exe", and right-click to inspect its properties. The path
@ -92,12 +92,12 @@ if (!require(Rphylip, quietly=TRUE)) {
# I have heard that your path must not contain spaces, and it is prudent to
# avoid other special characters as well.
# === 1.1.3 ... on Linux
# === 1.1.3 ... on Linux
# If you are running Linux I trust you know what to do. It's probably
# something like
# PROMLPATH <- "/usr/local/phylip-3.695/bin"
# === 1.1.4 Confirming PROMLPATH
# === 1.1.4 Confirming PROMLPATH
# Confirm that the settings are right.
PROMLPATH # returns the path
list.dirs(PROMLPATH) # returns the directories in that path
@ -106,7 +106,7 @@ list.files(PROMLPATH) # lists the files [1] "proml" "proml.command"
# If "proml" is NOT among the files that the last command returns, you
# can't continue. Ask on the mailing list for advice.
# == 1.2 Building a maxiiimum likelihood tree ==============================
# == 1.2 Building a maximum likelihood tree ================================
# Now read the mfa file you have saved in the BIB-PHYLO-Data_preparation unit,
# as a "proseq" object with the read.protein() function of the RPhylip package: