ProtML 2.3b3(July 1 1996) Maximum Likelihood Inference of Protein Phylogeny
Copyright (C) 1992-1996 J. Adachi & M. Hasegawa. All rights reserved.
Usage: protml [switches] sequence_file [topology_file]
sequence_file = MOLPHY_format | Sequential(-S) | Interleaved(-I)
topology_file = users_trees(-u) | constrained_tree(-e)
Model:
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j JTT (default) -jf JTT-F Jones, Taylor & Thornton(1992)
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d Dayhoff -df Dayhoff-F Dayhoff et al.(1978)
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m mtREV24 -mf mtREV24-F Adachi & Hasegawa(1995)
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p Poisson -pf Proportional (-f: with data Frequencies)
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r users RSR -rf users RSR-F (Relative Substitution Rate)
Search strategy or Mode:
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u Users trees (need users_trees file)
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R local Rearrangement search -RX LBP only
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e Exhaustive search (with/without constrained_tree file)
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s Star decomposition search (may not be the ML tree)
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q Quick add OTUs search (may not be the ML tree)
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D maximum likelihood Distance matrix --> NJDIST
Others:
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n num retained top ranking trees (default -e:105,-q:50)
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P num Per cent (default -e:30, if possible trees<=945 : 200)
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b no RELL-BP -M Minimum evolution (with -e)
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S Sequential format -I Interleaved format
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v verbose to stderr -i, -w output some information
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