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add TOC

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hyginn 2020-09-26 18:22:32 +10:00
parent b9ac373fce
commit 68b00c83e8
1 changed files with 13 additions and 13 deletions
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BIN-PHYLO-Tree_building.R
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@ -31,17 +31,17 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ----------------------------------------------------------- #TOC> -----------------------------------------------------------
#TOC> 1 Calculating Trees 46 #TOC> 1 Calculating Trees 48
#TOC> 1.1 PROMLPATH ... 66 #TOC> 1.1 PROMLPATH ... 68
#TOC> 1.1.1 ... on the Mac 71 #TOC> 1.1.1 ... on the Mac 73
#TOC> 1.1.2 ... on Windows 82 #TOC> 1.1.2 ... on Windows 101
#TOC> 1.1.3 ... on Linux 96 #TOC> 1.1.3 ... on Linux 115
#TOC> 1.1.4 Confirming PROMLPATH 101 #TOC> 1.1.4 Confirming PROMLPATH 120
#TOC> 1.2 Building a maximum likelihood tree 110 #TOC> 1.2 Building a maximum likelihood tree 134
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -70,7 +70,7 @@ if (! requireNamespace("Rphylip", quietly = TRUE)) {
# on your computer Phylip has been installed and define the path # on your computer Phylip has been installed and define the path
# to the proml program that calculates a maximum-likelihood tree. # 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 # On the Mac, the standard installation places a phylip folder
# in the /Applications directory. That folder contains all the # in the /Applications directory. That folder contains all the
# individual phylip programs as <name>.app files. These are not # individual phylip programs as <name>.app files. These are not
@ -98,7 +98,7 @@ if (! requireNamespace("Rphylip", quietly = TRUE)) {
# need to repeat this process. # need to repeat this process.
# #
# === 1.1.2 ... on Windows # === 1.1.2 ... on Windows
# On Windows you need to know where the programs have been installed, and you # On Windows you need to know where the programs have been installed, and you
# need to specify a path that is correct for the Windows OS. Find the folder # 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 # that is named "exe", and right-click to inspect its properties. The path
@ -112,12 +112,12 @@ if (! requireNamespace("Rphylip", quietly = TRUE)) {
# I have heard that your path must not contain spaces, and it is prudent to # I have heard that your path must not contain spaces, and it is prudent to
# avoid other special characters as well. # 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 # If you are running Linux I trust you know what to do. It's probably
# something like # something like
# PROMLPATH <- "/usr/local/phylip-3.695/bin" # PROMLPATH <- "/usr/local/phylip-3.695/bin"
# === 1.1.4 Confirming PROMLPATH # === 1.1.4 Confirming PROMLPATH
# Confirm that the settings are right. # Confirm that the settings are right.
PROMLPATH # returns the path PROMLPATH # returns the path
list.dirs(PROMLPATH) # returns the directories in that path list.dirs(PROMLPATH) # returns the directories in that path