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Dear @stephaneguindon, ./configure --enable-beagle ./configure: line 1: syntax error near unexpected token `(' ./configure: line 1: `m4trace:configure.ac:4: -1- AC_INIT([PhyML], [3.3.20230824], [[email protected]])'

liamxg

issue with mpirun after updating to Ubuntu 22

21

Dear Stephane, after updating two PCs from Ubuntu 18 to Ubuntu 22.04, PhyML stopped to work in both. No matter the command, it stops with message: ``` -------------------------------------------------------------------------- Primary job...

fermza

Building the BioNJ trees

5

Dear all, Is it possible to infer only the BioNJ trees given a sequence alignment? If so, what is the parameter setting for this? Thanks. Best, K.

KYQiu21

When I ran this program, it was stuck in a step and couldn't go forward. optimiz.c: 1601 alam = alam2 = f2 = fold2 = tmplam = .0; 1675 a=(rhs1/(alam*alam)-rhs2/(alam2*alam2))/(alam-alam2);...

ceceNo1

phytime compilation error

2

I am trying to build PhyML with --enable-phytime from last commit f3b45c4 and got this error: ``` gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -march=native -o phytime main.o utilities.o...

pavelToman

Smart Model Selection

2

Hello! I was wondering if Smart Model Selection (SMS) is an option in the command line? I did not see it in the manual. Please let me know. Thanks!

JamieBregman

which parameters should I use with the "lot of missing data"?

2

Dear @stephaneguindon, Could I know which parameters should I use with the "lot of missing data"? Thanks.

liamxg

How can I determine the optimal number of substitution rate categories to use?

3

Dear @stephaneguindon, How can I determine the optimal number of substitution rate categories to use? Thanks.

liamxg

how to enable `AVX`?

1

Dear @stephaneguindon, I hope this email finds you well! Could I know how to enable `AVX`? I am looking forward to your reply, thanks. Best, Liam

liamxg