Comments (1)
Hi,
-
Figure 1 in the main paper was made from
tree_species_distances.pdf
, meaning that this latter is the figure with branch lengths set to the rate-adjusted mixed Ks distances.
We used the more general description "branch length set to KS distances estimated from ortholog KS distributions" because some branches in the tree (for example those of O.sativa and A.comosus below) are not really part of the rate-adjustment that you see in the final Ks plot (there is no rate-adjusted ortholog Ks distribution between O.sativa and A.comosus). Note however that all branches are still computed through the relative rate test formulas (in that case using E.guineensis as outgroup), and are therefore estimated from the ortholog Ks distributions.
-
The Newick tree structure in
tree_species_distances.pdf
is the same given by the user in the configuration file, we only visually adapted the branch lengths.
Let us know if the answer is not clear. Thank you for posting the issue :)
from ksrates.
Related Issues (17)
- Error when executing ksrates test in nextflow HOT 5
- Incompatibility with recent Nextflow version HOT 4
- singularity HOT 5
- Issue with wgd paralog Ks analysis HOT 4
- TypeError: cannot convert the series to <class 'float'> HOT 10
- installation error HOT 2
- Warning: Dubious indirect gene relationship - closest genes get same color in alignment HOT 2
- ksrates paralogs-ks seemingly freezing on i-adhore step HOT 9
- ERROR Unexpected internal error during analysis of gene family GF_000001 HOT 4
- ERROR Unexpected internal error during analysis of gene family GF_000001 HOT 2
- ortholog_peak_db.tsv, ortholog_ks_list_db.tsv database are not generated HOT 2
- where would I find the equation or lognorm fit parameters to the Ks distributions? HOT 10
- Installation problem HOT 11
- No output files HOT 17
- Updated Errors HOT 11
- Difficulty in Output Plots Interpretation HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ksrates.