From 26db0ad62840cc1542930a103b0d0db0ee495f79 Mon Sep 17 00:00:00 2001 From: Maryam Hayati Date: Wed, 24 Jul 2019 13:35:32 -0700 Subject: [PATCH 1/4] Update README.md --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 03673c0..d0c0860 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,5 @@ These codes implement an improved version of the RF distribution computation by Here, we modified the dynamic programming algorithm introduced by Bryant et al for computing the distribution of RF distance for a given tree by leveraging the Number-Theoretic Transform (NTT), and improve the running time from O(l^5) to O(l^3log(l)), where l is the number of tips of the tree. Given an unrooted phylogenetic tree with l tips (T), the procedure for computing the RF distribution of this tree is as follow: Denote the node adjacent to tip l in T by v_0. Remove tip l, and root the resulting tree with v_0 as the root. We use this rooted tree as the input to the dynamic programming algorithm. -I will show how to compute the distribution of RF distance for a random tree with 8 tips using our implementations in R. The procedure is the same in python. From f6852ce1828cc868cc55414b8dcb34453f7d3fb2 Mon Sep 17 00:00:00 2001 From: Maryam Hayati Date: Wed, 24 Jul 2019 14:08:57 -0700 Subject: [PATCH 2/4] Update DESCRIPTION --- rfdistr/DESCRIPTION | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/rfdistr/DESCRIPTION b/rfdistr/DESCRIPTION index 61b584e..90362df 100644 --- a/rfdistr/DESCRIPTION +++ b/rfdistr/DESCRIPTION @@ -1,11 +1,10 @@ Package: rfdistr Type: Package -Title: What the Package Does (Title Case) +Title: RF distribution Version: 0.1.0 -Author: Who wrote it -Maintainer: The package maintainer -Description: More about what it does (maybe more than one line) - Use four spaces when indenting paragraphs within the Description. +Author: Maryam Hayati +Maintainer: The package maintainer +Description: These codes implement an improved version of the RF distribution computation by Bryant et al. Here, we modified the dynamic programming algorithm introduced by Bryant et al for computing the distribution of RF distance for a given tree by leveraging the Number-Theoretic Transform (NTT), and improve the running time from O(l^5) to O(l^3log(l)), where l is the number of tips of the tree. License: What license is it under? Encoding: UTF-8 LazyData: true From e1abe8a8a141192213d9dd0f9cf6e497d0211c8d Mon Sep 17 00:00:00 2001 From: Maryam Hayati Date: Wed, 24 Jul 2019 14:09:30 -0700 Subject: [PATCH 3/4] Update DESCRIPTION --- rfdistr/DESCRIPTION | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/rfdistr/DESCRIPTION b/rfdistr/DESCRIPTION index 90362df..91eac15 100644 --- a/rfdistr/DESCRIPTION +++ b/rfdistr/DESCRIPTION @@ -4,7 +4,10 @@ Title: RF distribution Version: 0.1.0 Author: Maryam Hayati Maintainer: The package maintainer -Description: These codes implement an improved version of the RF distribution computation by Bryant et al. Here, we modified the dynamic programming algorithm introduced by Bryant et al for computing the distribution of RF distance for a given tree by leveraging the Number-Theoretic Transform (NTT), and improve the running time from O(l^5) to O(l^3log(l)), where l is the number of tips of the tree. +Description: These codes implement an improved version of the RF distribution computation by Bryant et al. +Here, we modified the dynamic programming algorithm introduced by Bryant et al for computing the distribution of RF distance +for a given tree by leveraging the Number-Theoretic Transform (NTT), and improve the running time from O(l^5) to O(l^3log(l)), +where l is the number of tips of the tree. License: What license is it under? Encoding: UTF-8 LazyData: true From 299abad16b1cec1c2fbf5e688bfb863a0ac408c7 Mon Sep 17 00:00:00 2001 From: Frank Hui Date: Mon, 12 Aug 2019 18:11:15 -0700 Subject: [PATCH 4/4] Add installation procedure --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index 03673c0..de0a57b 100644 --- a/README.md +++ b/README.md @@ -6,3 +6,13 @@ Denote the node adjacent to tip l in T by v_0. Remove tip l, and root the result I will show how to compute the distribution of RF distance for a random tree with 8 tips using our implementations in R. The procedure is the same in python. +# Installation + +To install the python package, open a terminal and type:

+`pip install rfdist` + +To install the R package, open a terminal and type:

+`R`
+`install.packages("devtools")`
+`library("devtools")`
+`install_github("frankwhoee/rfdistr")`