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Home modified by john

john — Fri, 03 Oct 2025 14:34:29 -0000

--- v6
+++ v7
@@ -5,4 +5,4 @@

 See the first draft of the [Help Manual] to get started.

-People involved in this software are [John Archer](https://www.cibio.up.pt/en/people/details/john-archer/), [Pedro Esteves](https://www.cibio.up.pt/en/people/details/pedro-jose-esteves/),  [Joana Abrantes](https://www.cibio.up.pt/en/people/details/joana-abrantes/),  [James Harris](https://www.cibio.up.pt/en/people/details/david-james-alexander-edward-harris/),  [Raquel Linheiro](https://www.cibio.up.pt/en/people/details/raquel-linheiro/),  [Stephen Sabatino](https://www.cibio.up.pt/en/people/details/stephen-joseph-sabatino/)
+People involved in this software are [John Archer](https://www.cibio.up.pt/en/people/details/john-archer/), [Pedro Esteves](https://www.cibio.up.pt/en/people/details/pedro-jose-esteves/),  [Joana Abrantes](https://www.cibio.up.pt/en/people/details/joana-abrantes/), [Ana Margarida Lopes](https://www.cibio.up.pt/en/people/details/ana-margarida-lopes/),  [James Harris](https://www.cibio.up.pt/en/people/details/david-james-alexander-edward-harris/),  [Raquel Linheiro](https://www.cibio.up.pt/en/people/details/raquel-linheiro/),  [Stephen Sabatino](https://www.cibio.up.pt/en/people/details/stephen-joseph-sabatino/)

Home modified by john

john — Fri, 03 Oct 2025 14:29:31 -0000

--- v5
+++ v6
@@ -3,6 +3,6 @@

 TreeScope is a tool that increases the ease of rapidly interacting with sequence data at a highly detailed level. In this protype once the alignment has been loaded interactive trees can be readily created across various user selected section. Trees can be used to identify clusters from which nucleotide and amino acid frequencies can be easily, and immediately, extracted. Future developments will involve including recombination detection strategies using phylogenetic approaches as well as statistically comparing divergence rates across trees from different regions. At the moment an executable jar is available for download as well as some screenshots. Code will be made available on publication.

-An initial help manual is available here [Help Manual]
+See the first draft of the [Help Manual] to get started.

-People involved in this software are [John Archer](https://www.cibio.up.pt/en/people/details/john-archer/), [Pedro Esteves](https://www.cibio.up.pt/en/people/details/pedro-jose-esteves/),  [Joana Abrantes](https://www.cibio.up.pt/en/people/details/joana-abrantes/) and [Immunity and Emerging Disease Group](https://www.cibio.up.pt/en/groups/immunity-and-emerging-diseases-imed/) .
+People involved in this software are [John Archer](https://www.cibio.up.pt/en/people/details/john-archer/), [Pedro Esteves](https://www.cibio.up.pt/en/people/details/pedro-jose-esteves/),  [Joana Abrantes](https://www.cibio.up.pt/en/people/details/joana-abrantes/),  [James Harris](https://www.cibio.up.pt/en/people/details/david-james-alexander-edward-harris/),  [Raquel Linheiro](https://www.cibio.up.pt/en/people/details/raquel-linheiro/),  [Stephen Sabatino](https://www.cibio.up.pt/en/people/details/stephen-joseph-sabatino/)

Home modified by john

john — Fri, 03 Oct 2025 14:26:17 -0000

--- v4
+++ v5
@@ -3,4 +3,6 @@

 TreeScope is a tool that increases the ease of rapidly interacting with sequence data at a highly detailed level. In this protype once the alignment has been loaded interactive trees can be readily created across various user selected section. Trees can be used to identify clusters from which nucleotide and amino acid frequencies can be easily, and immediately, extracted. Future developments will involve including recombination detection strategies using phylogenetic approaches as well as statistically comparing divergence rates across trees from different regions. At the moment an executable jar is available for download as well as some screenshots. Code will be made available on publication.

+An initial help manual is available here [Help Manual]
+
 People involved in this software are [John Archer](https://www.cibio.up.pt/en/people/details/john-archer/), [Pedro Esteves](https://www.cibio.up.pt/en/people/details/pedro-jose-esteves/),  [Joana Abrantes](https://www.cibio.up.pt/en/people/details/joana-abrantes/) and [Immunity and Emerging Disease Group](https://www.cibio.up.pt/en/groups/immunity-and-emerging-diseases-imed/) .

Home modified by john

john — Mon, 14 Apr 2025 10:06:23 -0000

--- v3
+++ v4
@@ -2,3 +2,5 @@
 (Note: this is a protype tool and further details, including source code, will be provided on publication).

 TreeScope is a tool that increases the ease of rapidly interacting with sequence data at a highly detailed level. In this protype once the alignment has been loaded interactive trees can be readily created across various user selected section. Trees can be used to identify clusters from which nucleotide and amino acid frequencies can be easily, and immediately, extracted. Future developments will involve including recombination detection strategies using phylogenetic approaches as well as statistically comparing divergence rates across trees from different regions. At the moment an executable jar is available for download as well as some screenshots. Code will be made available on publication.
+
+People involved in this software are [John Archer](https://www.cibio.up.pt/en/people/details/john-archer/), [Pedro Esteves](https://www.cibio.up.pt/en/people/details/pedro-jose-esteves/),  [Joana Abrantes](https://www.cibio.up.pt/en/people/details/joana-abrantes/) and [Immunity and Emerging Disease Group](https://www.cibio.up.pt/en/groups/immunity-and-emerging-diseases-imed/) .

Home modified by john

john — Thu, 10 Apr 2025 13:23:00 -0000

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+++ v3
@@ -1,2 +1,4 @@
 **Overview**
+(Note: this is a protype tool and further details, including source code, will be provided on publication).
+
 TreeScope is a tool that increases the ease of rapidly interacting with sequence data at a highly detailed level. In this protype once the alignment has been loaded interactive trees can be readily created across various user selected section. Trees can be used to identify clusters from which nucleotide and amino acid frequencies can be easily, and immediately, extracted. Future developments will involve including recombination detection strategies using phylogenetic approaches as well as statistically comparing divergence rates across trees from different regions. At the moment an executable jar is available for download as well as some screenshots. Code will be made available on publication.

Home modified by john

john — Thu, 10 Apr 2025 13:18:43 -0000

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-Welcome to your wiki!
-
-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
-
-The wiki uses [Markdown](/p/treescope/wiki/markdown_syntax/) syntax.
-
-[[members limit=20]]
-[[download_button]]
+**Overview**
+TreeScope is a tool that increases the ease of rapidly interacting with sequence data at a highly detailed level. In this protype once the alignment has been loaded interactive trees can be readily created across various user selected section. Trees can be used to identify clusters from which nucleotide and amino acid frequencies can be easily, and immediately, extracted. Future developments will involve including recombination detection strategies using phylogenetic approaches as well as statistically comparing divergence rates across trees from different regions. At the moment an executable jar is available for download as well as some screenshots. Code will be made available on publication.

Home modified by John Archer

John Archer — Mon, 09 Sep 2024 10:29:03 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

John Archer (admin)