figtree | Library to manipulate figtree files

by MrJohz Rust Version: v0.2.2 License: MIT

X-Ray Key Features Code Snippets(1)Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | figtree Summary

figtree is a Rust library. figtree has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Figtree is a data format designed mainly for configuration with nodes and sections. It looks a bit like this:.

Support

Quality

Security

License

Reuse

Support

figtree has a low active ecosystem.

It has 9 star(s) with 1 fork(s). There are 3 watchers for this library.

It had no major release in the last 12 months.

figtree has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of figtree is v0.2.2

Quality

figtree has 0 bugs and 0 code smells.

Security

figtree has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

figtree code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

figtree is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

figtree releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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figtree Key Features

No Key Features are available at this moment for figtree.

figtree Examples and Code Snippets

Figtree - the noded config file,What is Figtree?

Rust

Lines of Code : 20

License : Permissive (MIT)

Copy

// C-style inline comments and block comments are allowed
myconfig {  // nodes consist of an identifier followed by a brace-block
    // each node can have a number of key-value attributes attached.
    // keys must be strings, but values can be stri

Community Discussions

Trending Discussions on figtree

What can be the reason of getting negative branches lengths after BEAST analysis?

Conda install Figtree

QUESTION

What can be the reason of getting negative branches lengths after BEAST analysis?

Asked 2022-Mar-28 at 10:51

I thought that BEAST does not allow negative lengths of branches on prior distribution level so I got very surprised when I have looked at my consensus tree in FigTree.

What could be the reason of this and how to wrestle with this phenomenon?

I am analysing about 1500 taxa of HAV (subtype: IA, region: VP1) under the next parameters: GTR+Г, Strict Clock, Coalescent constant population. Tree was generated by treeannotator through ~/beast/bin/treeannotator -heights median -burnin 20 -limit 0.5 VP1_test_bt_ExpPop.trees VP1_test_bt_ExpPop.tree

...

ANSWER

Answered 2022-Mar-28 at 10:51

I found the answer on ResearchGate from Santiago Sanchez-Ramirez & let me quote it here:

Try using the option -heights ca when you run TreeAnnotator. This stands for "common ancestor trees" and aims at summarizing clade ages across all posterior trees and not only the values for subset of trees that have that clade. If that subset of trees is low in frequency the average node height might end up being older than the direct ancestor. Here is the explanation for negative branches: "MCC trees produced by TreeAnnotator can have a descendent node that is older than its direct ancestor (a negative branch length). This may seem like an error but is actually the correct behaviour. The MCC tree is, by default, generated with average node heights across all trees in the sample which contain that clade. The negative branch lengths result when a clade is at low frequency and tends not to occur in those trees that have the MCC tree's ancestral clade (or vice versa). This means the average heights are for the adjacent nodes are derived from different sets of trees and may not have any direct ancestor-descendent relationship." In this paper you will find more information about the ca option: Looking for trees in the forest: Summary tree from posterior samples

Source https://stackoverflow.com/questions/71603918

QUESTION

Conda install Figtree

Asked 2020-Sep-27 at 04:13

Using Anaconda on Linux I tried this:

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ANSWER

Answered 2020-Sep-27 at 04:13

The Bioconda has channel configuration settings that users need to follow in order to get the expected behavior from Bioconda packages including solving for installs. In particular, users should have conda-forge > bioconda > defaults. This could be what is affecting the installation, since figtree has xorg-libxtst as a dependency and that is only on Conda Forge.

If you want to do this ad hoc (as in OP), the command that would mimic their recommended settings would be

Source https://stackoverflow.com/questions/64081302

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install figtree

You can download it from GitHub.
Rust is installed and managed by the rustup tool. Rust has a 6-week rapid release process and supports a great number of platforms, so there are many builds of Rust available at any time. Please refer rust-lang.org for more information.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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