1.2 Analysis of trees with dated tips Andrew Rambaut Andrew Rambaut, 2000. Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics. phylogeny tipdate outtree tipdate.out phylip_tree perl ! $notrees alignment Alignment file 10 perl " < $value" 11 readseq_ok_alig perl 1 control_options Control options 2 model MODEL (-m) F84 F84 HKY HKY REV REV F84 perl ($value and $value ne $vdef)? " -m$value" : "" constant_rate Molecular clock model (SR model) (-k) perl ($value) ? " -k" : "" change_rate_estim Estimate rate of change of rate (VRDT model: requires dated tips) (+w) +w VRDT model: requires dated tips (+w) +w+ Constrain to be +ve only (+w+) +w- Constrain to be -ve only (+w-) -w specify rate of change of rate (-w) perl ($value ne "-w") ? " $value" : "" change_rate_value perl ($change_rate_estim eq "-w") You may provide a change rate value (-w #) perl " -w $value" absolute_rate_estim Estimate absolute rate of substitution (SRDT model: requires dated tips) (+s) perl ($value) ? " +s" : "" absolute_rate_value perl (! $absolute_rate_estim) You may provide an absolute rate of molecular evolution (requires dated tips) (-s) perl ($value) ? " -s $value" : "" likelihood_root_estim Estimate maximum likelihood root (requires molecular clock) perl ($value) ? " +r" : "" likelihood_root_value perl (! $likelihood_root_estim) root with specified outgroup taxa (requires molecular clock) (-r #) perl ($value) ? " -r $value" : "" outgroup perl (! $estimate_root) and $constant_rate Root with specified outgroup taxa (requires molecular clock) (-r) perl (defined $value)? " -r $value" : "" substitution_confidence Estimate confidence intervals for rate of substitution (with +s option) (-is) perl ($value)? " -is" : "" date_confidence Estimate confidence intervals for date of root of tree (with +s option) (-id) perl ($value)? " -id" : "" change_confidence Estimate confidence intervals for rate of change of rate of substitution (with +w option) (-iw) perl ($value)? " -iw" : "" limit Limit to use estimating confidence intervals (-l) 1.92 perl (defined $value and $value != $vdef)? " -l $value" : "" codon_categories CODON CATEGORIES = 112, 123, 120, etc. [default: homogeneity] (-p) perl ($value)? " -p $value" : "" codon_rate CODON category rates: #1 #2 #3 separated by commas [default = estimate rates] (-c) perl ($value)? " -c$value" : "" seperate Estimate seperate models for each site category (-e) perl ($value)? " -e" : "" gamma Num categories for gamma rate heterogeneity (2 to 32) (-g) Enter an integer between 2 and 32 that specifies the number of categories to use with the discrete gamma rate heterogeneity model. perl (defined $value)? " -g $value" : "" alpha perl $gamma gamma shape (alpha) for site rate heterogeneity (-a) perl (defined $value)? " -a $value" : "" datasets Number of Datasets (-n) 1 perl (defined $value and $value != $vdef)? " -n $value" : "" user_branch User branch-lengths [default = estimate] (-ul) perl ($ value) ? " -ul" : "" treefile Optional file containing trees perl ($value)? " $value":"" 5 equal_freq Frequences of bases equal (-f=) perl ($value)? " -f=" : "" freq_bases perl ! $equal_freq Frequences of bases: #A #C #G #T separated by commas(-f) perl ($value)? " -f$value" : "" transition_transversion Transition/transversion ratio (-t) 2.0 perl (defined $value and $value != $vdef)? " -t$value" : "" output_options Output options 3 branch Print final branch lengths (-vb) perl ($value)? " -vb" : "" likelihoods Write likelihoods for each Site (-vs) perl ($value)? " -vs" : "" notrees Don't Write trees (-vw) perl ($value)? " -vw" : "" memory Memory usage information (-vm) perl ($value)? " -vm" : "" progress perl " -vp"