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Posted by / 08-Feb-2020 11:37

The code h dating

In order to have unique solution, at least two different precise values of dates should be given.

Therefore, a tree with all tips having the same date and no further date information on internal nodes will not able to estimate absolute dates.

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nexus : trees in nexus format where branch lengths are measured rescaled to time unit by multiplying with the estimated rate.

ACE, American, American Hardware, America's Best, Apex, Aqua Temp, Aqua Therm, Aquamatic, Best, Best Deluxe, Champion, Craftmaster, De-Limer, Deluxe, Eagle, The Earl's Energy Conservation Water Heater, The Earl's Energy Saver Plus, Envirotemp, Four Most, Hotmaster, Hotstream, King-Kleen, King-Line, Master Plumber, Nationaline, Neptune, Penquin, Premier Plus, Premier Plus Self Cleaning Prestige, Pro Line and Pro Line Plus, Quaker, Quick-Flo, Raywall, Revere, Riveria, Sands, Sentinal, Servi-Star, Shamrock, Special Deluxe, Standard, Super Eagle, Super-Flo, Supreme, Sure-Fire, Thoro-Clean, Tru-Test, Tru Value, U. Supply, Whirlpool, XCL Energy Saver Ace, American Hardware, America's Best, Apex, Aqua Temp, Aqua Therm, Aquamatic, Best, Best Deluxe, Craftmaster, De-Limer, Deluxe, Eagle, The Earl's Energy Conservation Water Heater, The Earl's Energy Saver Plus, Envirotemp, Four Most, Hotmaster, Hotstream, King-Kleen, King-Line, Master Plumber, Nationaline, Neptune, Penquin, Prestige, Pro-Line, Pro-Line Plus, Quaker, Quick-Flo, Raywall, Revere, Riviera, Sands, Sentinal, Servistar, Shamrock, Special Deluxe, Standard, Supereagle, Super-Flo, Supreme, Sure-Fire, Thoro-Clean, True-Test, Tru Value, U.

The file should have each rate per line which corresponds to each tree in the Input_tree_file, for example: If there are more than 1 outgroups, than they must be monophyletic in the input trees.

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It should be noticed that LSD always assumes an increasing-time order from root to tips, i.e the date of a node is smaller than that of its children. The input file must contain one tree per line: An input date file is optional.

You can also use the pre-compiled files in the `bin` folder but sometimes it might not work if the configuration of your -a root_date -z leaves_date (to estimate relative dates) further options can be specified (-f -o -c -v -n -r -g -p ...). Option -c is recommended to take into account the temporal constraints (date of a node = date of its ancestors).

If there's not any tip defined, then the subtree is extended down to the tips of the full tree.

Hence, defines the subtree rooted at the node n1; and defines the subtree rooted at n5 that has one tip as n4 and other tips as the ones of the full trees (here are B, C).

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LSD: LEAST-SQUARES METHODS TO ESTIMATE RATES AND DATES FROM SERIAL PHYLOGENIES - v0.3beta by Thu-Hien TO If you use this software, please cite: “ Fast dating using least-squares criteria and algorithms”, T-H. If the input date is provided, the program estimates will the absolute dates.