New programs. Waiting list. Other lists. Old programs. Not listed. L ist of packages arranged T able of contents by methods available. General-purpose packages Parsimony programs Distance matrix methods Computation of distances Maximum likelihood methods Bayesian inference methods Quartets methods Artificial-intelligence and genetic algorithms methods Invariants or Evolutionary Parsimony methods Interactive tree manipulation Looking for hybridization or recombination events Bootstrapping and other measures of support Compatibility analysis Consensus trees, subtrees, supertrees, distances between trees.
T able of contents by computer systems on which they work. A nalyzing particular types of data. R ecent listings. List is currently empty because I have been unable to do much updating owing to other pressures so no new packages have been added in the last year.
R ecent changes. LVB 19 June O ther lists of phylogeny software. N ew programs waiting to be added. Moleculoid 9. Heuristics Choosing heuristics brings up the following window:. Maximum trees to keep: This lets you set the number of trees to be kept in memory.
The default is , and the maximum allowed by the program is Number of replications: Set the number of times you want the program to randomize the order of the taxa, create a cladogram, and submits it to branch-swapping storing in memory as many trees as set in the previous box. Starting trees: This determines the maximum number of trees to keep in each replication of branch- swapping.
Random seed: The program uses a pseudo-random number generator to randomize addition sequences. The default is to just use the time as the seed for the first replication. Name of Stem: enter a name of a file where the output will be written.
Two different files are created. The first with the. The second with the. The Search Strategy box allows you to fine tune the way in which the search is conducted: a. Multiple TBR - searches for trees using tree bisection-reconnection method of branch-swapping. Most programs go through a long slow procedure in which much time is spent collecting and swapping on large islands of trees that differ by minor rearrangements of a few taxa.
What strategies can be used to avoid this problem? Maximize the number of distinct starting trees e. Reduce the number of trees kept during each replication e.
Collect the results and then branch swap for more complete results e. Rachet or island hopper - maximizes finding new starting points - reduces the amount of time spent on each new search - retains the most parsimonious trees. An initial tree is obtained. This is used as the initial lowest bound for number of steps. Weights are reset to original and the tree is swapped to find the optimal tree at that island. If trees are treated as polytomous, swapping takes a longer time per tree than simply comparing whether the trees have different unsupported dichotomous resolutions, but when branches are collapsed fewer trees may have to be swapped if the data produce unresolved clades.
One additional modification of the rachet reported by Nixon is that it can be made more effective in finding islands by randomly constraining a subset of groups during each iteration. When complete the program automatically defaults to Windada and the shortest trees found are shown.
Homogeneity is measured using the incongruence length difference test Mickevich and Farris, :. DXY is 0 when the two data sets agree on the same tree; it is large when minimizing homoplasy in one data set increases the other. This method works by resampling smaller data sets from the combined data set. If there is significant disagreement between the two data sets, the added lengths of the resampled matrices will be significantly longer than the tree lengths of the original matrices.
The matrix is resampled many times and a statistic is produced which, if the length incongruence of the resampled matrices is smaller than the observed length incongruence, the null hypothesis that the data sets are congruent is rejected. A dialog box will open:. This is not a most parsimonious tree - it is just a ladder-like tree of your data.
If more than one tree results from an analysis, you can scroll through the different trees using these keys:. Use the last button to jump back to the Windada dataset window:.
Black circles indicate nonhomplasious changes synapomorphies or autapomorphies. White circles show homoplasies this dataset has no homoplasy.
If character and state names have been entered as information, words instead of numbers can be used to label branches:. Arrow keys allow you to click and scroll through all the different characters:. Add a new character to the data set, in which the outgroup has one state and the ingroup members all have another:. A common misconception is that this is a synapomorphy that shows the monophyly of the ingroup, but it is also possible that the state in the ingroup is plesiomorphic and the alternative state in the outgroup is derived in other words, it is an apomorphy for the outgroup.
To illustrate ambiguous optimization, create a matrix with the following data:. There is only one tree for the data, but the optimization of the last character is ambiguous. Fast optimization puts the change on the tree as soon as possible. Slow optimization puts the change on the tree as late as possible. The Downward Pass Beginning with the terminal taxa and proceeding towards the root node, assign characters to the ancestral nodes according to the following rules:.
If both states are equally common then assign both states. The Upward Pass Begin to work from the root node upward, applying the following rules:.
Beginning with the terminal taxa and proceeding towards the root node, assign characters to the ancestral nodes according to the following rules:. Confusion still persists about the way in which NONA stores trees. Winclada simple reads a tree file - and if the trees are dichotomous, it displays them as such. However, under the default optimization unambiguous changes only if characters are mapped there will be no character changes at those nodes.
Note, that under FAST or SLOW optimization, branches that have a minimum length 0 may still have length under that particular optimization, and will be shown as such. Trees may be also saved as already collapsed by NONA by saving with the ksv command instead of sv command. This alleviates the problem of collapsing branches, but note that it will not be possible to recover those nodes within Winclada unless you manually reinstate them with the mouse.
Thus, these trees may be reported as having more steps than thought when read into Winclada or back into NONA. Printing Trees 1. Use arrow keys, zoom keys, etc to make the tree look the way you want it to on the page 4. F3 - Contract tree on X axis. This function squeezes the hashmarks closer together and shortens the branches incrementally. F4 - Expand tree on X axis.
This function spreads out the hashmarks and lengthens the branches incrementally. F5 - Contract tree on Y axis. This function shortens the distance between adjacent branches, making the tree shorter in the vertical axis. F6 - Expand tree on Y axis. This function increases the distance between adjacent branches, making the tree longer in the vertical axis.
F7 - Move to previous tree in ram. F8 - Move to next tree in ram. This has the effect of increases the angle or degree of curvature e. In either gothic or jetclad trees, decreasing this will eventually result in a rectangular clados style tree. This not only affects the size of the tree on the screen, but also has a direct effect on the size of the tree printed.
See printing recommendations below, however. Unlike z and SHIFT-Z, which change the size of the tree as printed on the page, this zooming function just affects your view of the page. This allows you to scale the view to see the entire page, and will allow viewing of multiple pages in future versions….
Some of the commands are obvious, and I have not been anal enough yet to write out what each one of these does. File Open file Opens a window that lets you open a data file. Interface Windada Go to the Tree editor. Cpanel Scroll through the distribution of character states in the taxa.
Tpanel Scroll through character districutions or make block changes to groups of taxa Key Use the data to construct an identification key.
Matrix Go to next matrix F12 Several different data files can be open at once, but they can only be worked on one at a time. This lets you hide one file and bring another into view so that it can be edited or analyzed. New matrix create create a new matrix. Save Overwrite the matrix with new data a new matrix must be first saved in either Nona or Winclada format Save as Nona format. Unselect current matrix Keep a file open, but do not send it to be analyzed. Select all matrices When several files need to be combined or analyzed with the ILD test, open them all and then select them all.
Expand matrix Opens a dialog box that lets you expand the data matrix by adding more characters or more taxa or both. Set token key for matrix To set matching for data merges. Matrix dialog Enter character and state names, activate and deactivate characters, and make characters additive or non-additive Comment dialog Enter information, in paragraph form, about the matrix not to exceed characters.
If I have several matrices that differ just in the way some characters or taxa are treated, I record what I need to remember for and particular file in this dialog box. Comment list A list of all the Comment dialogs for the matrix. Flag Cells Add color to cells to highlight? Edit Locked no data entry.
Enter polymorphisms A dialog box allows you to click all the states that apply to the character and taxon indicated by the cursor in the data matrix Sort by taxon names Put taxa in alphabetical order.
Find and replace cell value For the row of data indicated by the cursor, you can have one state value replace by another Find terminal Jump to a taxon. Terms Taxon dialog Enter taxon names and set the ambiguity filter on or off. Select taxa by scope Scopes are command lines that define a range of parameters e. Activate selected taxa. Characters Character dialog Enter names of characters and states, activate and deactivate characters, and make them additive or nonadditive, or selected and unselected GoTo character.
Invert selected characters All characters that were previously selected are unselected, and those previously not selected are selected.
Activate selected characters Choose the characters that should be active in a data analysis. Deactivate selected characters Choose the characters that should not be active in a data analysis. Weight characters A dialog box opens that allows you to set the weight for a range or a single character Scale character weights?
Enter an integer value what does this then do?? For a character with states 0,1, and 2: state 0 to 1 is one step but 0 to 2 is two steps.
For a character with states 0,1, and 2: transformation between any two states is one step. Copy selected characters Duplicates selected characters and adds them to the end of the data matrix. Mop uninformative chars select characters that are uninformative be careful with this!
View Share char statistics Shows at the top of the screen information for each character, including: - number of informative steps possible in the character - maximum number of steps in the character if optimized on a bush - minimum number of steps in the character - weights for each character - whether the character is activated or not activated - whether the character is currently set as additive or nonadditive Refresh screen As you do different things with color and selecting things, bits of lines and colors may fail to completely erase.
Refresh will wipe these bits out and make the view clear again command dialog? Cursor settings Brings up a dialog box in which the top three buttons determine which direction the cursor moves if at all.
The next three buttons change the way the cursor looks during data entry. The next buttons allows the taxon name or character state to follow right behind the cursor.
You can also change the colors of the data at the cursor position. Matrix background colors. Change state foreground colors This makes it the different states stand out - and is very helpful if you are using Winclada to refine alignments Change state background colors This makes it the different states stand out - and is very helpful if you are using Winclada to refine alignments Change taxon select color.
Select taxa ambiguous for selected characters Spawn Send data to another program. Moleculoid Various commands for aligning and treating gaps Kill Stops new rachet iterations from forming and finishes the existing runs. Export tab-delimited matrix Creates a file of taxa, characters and the states for each taxon. Because tabs separate each field, the data set can be read by Excell and other common spreadsheets Export Fasta File. Open navigation menu.
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