From c1938b0e7ffd7762d78106a31951aa1792646d0a Mon Sep 17 00:00:00 2001 From: heche-psb Date: Wed, 22 May 2024 06:38:23 +0200 Subject: [PATCH] README update --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f23139d..65d171f 100644 --- a/README.md +++ b/README.md @@ -1006,12 +1006,14 @@ Here we only implemented the concatenation analysis using protein sequence by ad INFO Done cli.py:242 ``` -To visualize the date, we also provided a python script to plot the WGD dates in the `wgd` folder. Users need to extract the raw dates from the `mcmc.txt` for the WGD node first and save it as file `dates.txt` (or whatever preferred name). An example command is as below. +To visualize the date, we also provided a python script to plot the WGD dates in the `wgd` folder. Users need to extract the raw dates from the `mcmc.txt` for the WGD node first and save it as file ![](dates.txt) (or whatever preferred name). An example command is as below. ``` python $PATH/postplot.py postdis dates.txt --percentile 90 --title "WGD date" --hpd -o "Ranunculales_WGD_date.svg" ``` +Users can freely set the percentile for CI (either in HPD with `--hpd` or in Equal-Tailed CI without `--hpd`) and the title and output file name via `--title` and `-o`. + ![](data/Ranunculales_WGD_date.svg) The posterior mean, median and mode of the Ranunculales WGD age is 112.92, 113.44 and 112.54 mya, with 90% HPD 105.07 - 122.32 mya as manifested above.