2.3b3 ProtML, NucML phylogeny programs J. Adachi & M. Hasegawa phylogeny prot_nucml prot_nucml Program protml protml nucml nucml perl "$value" nucml 0 ProtML: Maximum Likelihood Inference of Protein Phylogeny NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny interleaved perl " -I" 1 tee perl " | tee molphy.results | sed -n \\"/;/p\\" " 1000 results "molphy.results" phylip_dist perl $mode eq "-D" outtree perl " > outtree" "outtree" 1100 phylip_tree perl ! $info sequences Sequences File (protml or nucml) perl " $value" 3 Sequences file default format: interleaved (analog to Phylip format) 12 perl ( $prot_nucml eq "protml" || $prot_nucml eq "nucml" ) readseq_ok_alig perl 1 model Model (ProtML or NucML) perl ( $prot_nucml eq "protml" || $prot_nucml eq "nucml" ) modelprot Model for ProtML -j JTT (Jones, Taylor & Thornton) (-j) -jf JTT-F (Jones, Taylor & Thornton) (-jf) -d Dayhoff (Dayhoff & al) (-d) -df Dayhoff-F (Dayhoff & al) (-df) -m mtREV24 (Adachi & Hasegawa) (-m) -mf mtREV24-F (Adachi & Hasegawa) (-mf) -p Poisson (-p) -pf Proportional (-pf) -r users RSR (Relative Substitution Rate) (-r) -rf users RSR-F (-rf) -f with data Frequencies (-f) perl ($prot_nucml eq "protml" ) perl ($value ne $vdef)? " $value" : "" -j 1 modeldna Model for NucML -t Alpha/Beta (Hasegawa, Kishino & Yano) and/or AlphaY/AlphaR (Tamura & Nei) (-t) -p Proportional (-p) -pf Poisson (-pf) -r users RSR-F (Relative Substitution Rate) (-r) -rf users RSR (-rf) -f -f withOUT data Frequencies perl ( $prot_nucml eq "nucml" ) perl ($value ne $vdef)? " $value" : "" -t 1 n1 n1 : Alpha/Beta ratio (default:4.0) (option : -t n1) perl ($prot_nucml eq "nucml" && $modeldna =~ /^-t/) perl (! defined $n2 && defined $n1)? " -t $n1":"" 4.0 1 n2 n2 AlphaY/AlphaR ratio (default:1.0) (option : -t n1,n2) perl ($prot_nucml eq "nucml" && $modeldna =~ /^-t/) perl (defined $n1 && defined $n2)? " -t $n1,$n2":"" 1.0 1 search Search strategy or Mode (ProtML or NucML) mode Strategy or Mode -u Users trees (need users_trees file) (-u) -R local Rearrangement search (-R) -RX LBP (local bootstrap probability only) (-RX) -e Exhaustive search (with/without constrained_tree file) (-e) -s Star decomposition search (may not be the ML tree) (-s) -q Quick add OTUs search (may not be the ML tree) (-q) -D maximum likelihood Distance matrix (for NJDIST) (-D) perl " $value" -q 1 topology Topology File (if Users Tree mode or Exhaustive search or local Rearrangement search) this file must contain the number of tree(s) perl ($mode eq "-u" || $mode eq "-e" || $mode eq "-R" ) perl ($value)? " $value" : "" 4 output Output Parameters num Retained top ranking trees (-n) perl (defined $value)? " -n $value":"" 1 You should enter an integer value perl $value !~ /^\\d*$/ verbose Verbose to stderr (-v) perl ($value)? " -v":"" 1 info Output some informations (-i -w) perl ($value)? " -i -w":"" 1 others Others Options boot no Bootstrap probabilities (Users trees) (-b) perl ($value)? " -b":"" 1 perl ($mode =~ /^-u/ ) minimum_evolution Minimum evolution (with -e) (-M) perl ($value)? " -M":"" 1 perl ($mode =~ /^-e/ ) sequential Sequential format (-S) perl ($value)? " -S":"" 1