chriscurrin / nrevanalysis Goto Github PK

#Introduction NREVanalysis is used to check (and generate) the best phylogenetic tree, where GTR is favoured compared against NREV6 and NREV12 models ##Installation At the moment, only Linux is supported

HYPHY have released a Windows binary, so it is possible to port to Windows (this was a previous limitation)

run the following in the terminal (will need sudo privileges; bash sometimes optional) bash installRequiredLibs bash installHyPhy

####FastTree Try provided binaries:

• type in the terminal: <full directory>/FastTree or <full directory>/FastTreeMP (e.g. if NREVanalysis is located in Documents folder then open a terminal and type ~/Documents/NREVanalysis/FastTree/FastTreeMP)
• if the response is multiple lines (i.e. shows how to use the program) then the file is compatible with the system
• the first output line should be 'Usage for FastTree version...' etc.
• if there is an error such as cannot find the command or must install the program, compile by running: bash installFastTree (see file in editor for details)
• if you'd like FastTree to be slightly more accurate in generating the initial tree, recompile FastTree with -DUSE_DOUBLE

finally run: javac *.java

Alternative, run bash install which does the previous steps for you, but will build FastTree explicitly