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While most Tree-Comparison software is focused on binary comparisons, which is the comparison between the topologies of two single sequences, Path-O-Gen is focused on the comparison of patriclines, or the comparison between the paths that can be drawn in the trees. Paths can be drawn (for example) in the following ways:
comparing the shapes of nonbinary clades in the topologies.
analysing gene trees. In such analyses, the patricline traverses one gene at a time as well as several codon positions. Typically, the patriclines are drawn or read from the most conserved position to the less conserved.
investigating the number of independent rearrangements that have occurred in the history of a gene. Such rearrangements are typically counted based on fixed differences and are usually called “indels” (insertions and deletions). However, it has been noticed that indels can be hard to calculate reliably. A solution is to detect apparent rearrangements in a gene tree (say, a translocation) and to calculate the likelihood of the events that would lead to the rearrangement. The probabilities of these rearrangements are then compared to all possible rearrangements, allowing the computation of statistical significance. This approach is called “time-likelihood” and is implemented in Path-O-Gen.
The software is designed to compare trees and patriclines, two different things, so Path-O-Gen has some features that are optimized to the analysis of patriclines.
Here are the main features:
Path-O-Gen will compare two or more trees using the standard reciprocal-neighbor-joining (NJ) algorithm. However, this algorithm assumes a molecular clock. Thus, it is possible to compare patriclines using the NJ algorithm, not requiring a molecular clock (there are a few other tree-comparison methods that work without a molecular clock, such as subtree pruning regrafting (SPR)).
The patriclines of the trees that are compared will be displayed using tics, which are the time points at which rearrangements occur. Tics will automatically indicate where branches are missing, so that paths can be drawn.
A Tree-O-Gram gives a graphical impression of the shape of the patricline, with the patricline being laid out in the order in which the rearrangements occurred. For each patricline,
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This program reads in a phylogenetic tree as input and examines whether there is enough temporal signal to estimate the rate at which genetic change occurs among lineages.
If too little is present, then you know that the tree has not undergone the clock assumption.
If sufficient temporal signal is present, then you can estimate a clock rate and use this rate to date the tree at tip-nodes.
The user has the option of selecting the informative nodes in the tree by hand, by clicking on them in the tree or by using the expression /rate-tree. A value of 1 is always used.
The program also uses the Date-It R package to find the likely time of origin of each sequence.
Once a rate is estimated for each node, Path-O-Gen also calculates the importance of each node in the tree using the False-Positive and False-Negative Rates. These are both represented by the relative lengths of the corresponding branch lengths.
This program exports the output of the Path-O-Gen program to a file and converts the number of substitutions per site to a number of years using a molecular clock rate and then calculates the time of origin for each sequence.
Trees without Clock Assumption:
Dated-tip phylogenies have little value without using the assumption that the tree has undergone the molecular clock.
Trees with Little Temporal Signal:
Dated-tip phylogenies are easy to analyze because they are free of assumptions about molecular clock.
But if the tree did not have enough temporal signal, then the molecular clock assumption might not be correct.
This can be investigated by running the Path-O-Gen program on the tree.
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What’s New in the Path-O-Gen?
The main goals of Path-O-Gen are to:
analyze the quality of phylogenetic signal and how this compares to what we would expect from a true clock; and calculate the probable divergence times and the confidence intervals of these times.
The program can also infer the most clock-like tree it can find.
Path-O-Gen automatically performs all the tree manipulations and tests that it needs to carry out (gaps, poorly supported nodes, deep tree-ward ing etc.) in order to adequately detect violations of clocklike topologies or rejection of the molecular clock assumption.
Molecular clock-aware tree manipulations
Unless explicitly told by the user, Path-O-Gen would assume that a tree has undergone (near) neutral evolution during its phylogenetic history. This means that the tree cannot be manipulated without artificially affecting the tree’s date estimate.
When a tree is known to have been clock-like, Path-O-Gen can edit dates on tree leaves to create time-series trees. When dealing with collections of contemporaneous sequences, the age of the tips can vary and it is important to know what these ages are so as to distinguish between them.
Change the date of all tree leaves at once using the ‘Date Range’ dialog.
Create a time-series tree and assign the sampled ages as nodes. You may then go back to the ‘Date Range’ dialog to change the ages again.
The ages that appear in the tree will be values in years, months and days since the tree root.
Root the tree at a point before the most recent common ancestor.
Use the ‘Root’ button to choose where to root the tree.
If your root position is not clock-like, the time-series tree tool will give you a warning at the root. If you move the root to a better position, you can re-root the tree.
Time-series tree tool
If the tree has been clock-like, the date-range tool creates a time-series tree that contains the sampled dates at the leaves of the tree. This tree is useful when you want to compare the differences between trees of the same but different times.
The tree can be rooted at an arbitrary time.
Time interval statistics
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Multiplayer games for local play between up to four players.
Joysticks are supported.
High-resolution display recommended.
Optional keyboard and mouse support.
Minimum required system specification:
Processor: 3.6 GHz Intel Core i3
Memory: 4 GB (RAM)
Graphics: 1 GB NVIDIA GeForce 8800 GTX, AMD Radeon HD 4870 (2 GB VRAM)