nodeSub (Q80333): Difference between revisions

← Older edit

@@ Property / programmed in @@
-R
@@ Property / programmed in: R / rank @@
-Normal rank
@@ Property / last update @@
-August 2022Timestamp +2022-08-19T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2022-08-19T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / last update: 19 August 2022 / rank @@
-Normal rank
@@ Property / author @@
-Thijs Janzen
@@ Property / author: Thijs Janzen / rank @@
-Normal rank
@@ Property / copyright license @@
-GNU General Public License, version 3.0
@@ Property / copyright license: GNU General Public License, version 3.0 / rank @@
-Normal rank
@@ Property / depends on software @@
-Rcpp
@@ Property / depends on software: Rcpp / rank @@
-Normal rank
@@ Property / depends on software @@
-ape
@@ Property / depends on software: ape / rank @@
-Normal rank
@@ Property / imports @@
-apTreeshape
@@ Property / imports: apTreeshape / rank @@
-Normal rank
@@ Property / imports @@
-phangorn
@@ Property / imports: phangorn / rank @@
-Normal rank
@@ Property / imports @@
-tibble
@@ Property / imports: tibble / rank @@
-Normal rank
@@ Property / imports @@
-DDD
@@ Property / imports: DDD / rank @@
-Normal rank
@@ Property / imports @@
-Rmpfr
@@ Property / imports: Rmpfr / rank @@
-Normal rank
@@ Property / imports @@
-assertthat
@@ Property / imports: assertthat / rank @@
-Normal rank
@@ Property / imports @@
-pbapply
@@ Property / imports: pbapply / rank @@
-Normal rank
@@ Property / imports @@
-phylobase
@@ Property / imports: phylobase / rank @@
-Normal rank
@@ Property / imports @@
-geiger
@@ Property / imports: geiger / rank @@
-Normal rank
@@ Property / imports @@
-babette
@@ Property / imports: babette / rank @@
-Normal rank
@@ Property / imports @@
-beautier
@@ Property / imports: beautier / rank @@
-Normal rank
@@ Property / imports @@
-beastier
@@ Property / imports: beastier / rank @@
-Normal rank
@@ Property / imports @@
-mauricer
@@ Property / imports: mauricer / rank @@
-Normal rank
@@ Property / imports @@
-tracerer
@@ Property / imports: tracerer / rank @@
-Normal rank
@@ Property / imports @@
-rappdirs
@@ Property / imports: rappdirs / rank @@
-Normal rank
@@ Property / imports @@
-testit
@@ Property / imports: testit / rank @@
-Normal rank
@@ Property / imports @@
-stringr
@@ Property / imports: stringr / rank @@
-Normal rank
@@ Property / cites work @@
-Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation
-Normal rank
@@ Property / software version identifier @@
+.2.2
@@ Property / software version identifier: 1.2.2 / rank @@
+Normal rank
@@ Property / software version identifier: 1.2.2 / qualifier @@
+publication date: 11 January 2022Timestamp +2022-01-11T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2022-01-11T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.2.3
@@ Property / software version identifier: 1.2.3 / rank @@
+Normal rank
@@ Property / software version identifier: 1.2.3 / qualifier @@
+publication date: 1 February 2022Timestamp +2022-02-01T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2022-02-01T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.2.4
@@ Property / software version identifier: 1.2.4 / rank @@
+Normal rank
@@ Property / software version identifier: 1.2.4 / qualifier @@
+publication date: 24 May 2022Timestamp +2022-05-24T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2022-05-24T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.2.7
@@ Property / software version identifier: 1.2.7 / rank @@
+Normal rank
@@ Property / software version identifier: 1.2.7 / qualifier @@
+publication date: 15 September 2023Timestamp +2023-09-15T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2023-09-15T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.2
@@ Property / software version identifier: 1.2 / rank @@
+Normal rank
@@ Property / software version identifier: 1.2 / qualifier @@
+publication date: 30 September 2021Timestamp +2021-09-30T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2021-09-30T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / software version identifier @@
+.2.8
@@ Property / software version identifier: 1.2.8 / rank @@
+Normal rank
@@ Property / software version identifier: 1.2.8 / qualifier @@
+publication date: 14 November 2023Timestamp +2023-11-14T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2023-11-14T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / programmed in @@
+R
@@ Property / programmed in: R / rank @@
+Normal rank
@@ Property / last update @@
+November 2023Timestamp +2023-11-14T00:00:00Z
Timezone +00:00
Calendar Gregorian
Precision 1 day
Before 0
After 0
-Timestamp
++2023-11-14T00:00:00Z
-Timezone
++00:00
-Calendar
+Gregorian
-Precision
+day
 Before
 After
@@ Property / last update: 14 November 2023 / rank @@
+Normal rank
@@ Property / description @@
+Simulate DNA sequences for the node substitution model.    In the node substitution model, substitutions accumulate additionally     during a speciation event, providing a potential mechanistic explanation for     substitution rate variation. This package provides tools to simulate    such a process, simulate a reference process with only substitutions along    the branches, and provides tools to infer phylogenies from alignments. More    information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
+Normal rank
@@ Property / author @@
+Thijs Janzen
@@ Property / author: Thijs Janzen / rank @@
+Normal rank
@@ Property / copyright license @@
+GNU General Public License, version 3.0
@@ Property / copyright license: GNU General Public License, version 3.0 / rank @@
+Normal rank
@@ Property / depends on software @@
+Rcpp
@@ Property / depends on software: Rcpp / rank @@
+Normal rank
@@ Property / depends on software @@
+ape
@@ Property / depends on software: ape / rank @@
+Normal rank
@@ Property / imports @@
+phangorn
@@ Property / imports: phangorn / rank @@
+Normal rank
@@ Property / imports @@
+tibble
@@ Property / imports: tibble / rank @@
+Normal rank
@@ Property / imports @@
+DDD
@@ Property / imports: DDD / rank @@
+Normal rank
@@ Property / imports @@
+Rmpfr
@@ Property / imports: Rmpfr / rank @@
+Normal rank
@@ Property / imports @@
+pbapply
@@ Property / imports: pbapply / rank @@
+Normal rank
@@ Property / imports @@
+phylobase
@@ Property / imports: phylobase / rank @@
+Normal rank
@@ Property / imports @@
+geiger
@@ Property / imports: geiger / rank @@
+Normal rank
@@ Property / imports @@
+beautier
@@ Property / imports: beautier / rank @@
+Normal rank
@@ Property / imports @@
+beastier
@@ Property / imports: beastier / rank @@
+Normal rank
@@ Property / imports @@
+tracerer
@@ Property / imports: tracerer / rank @@
+Normal rank
@@ Property / imports @@
+rappdirs
@@ Property / imports: rappdirs / rank @@
+Normal rank
@@ Property / imports @@
+testit
@@ Property / imports: testit / rank @@
+Normal rank
@@ Property / imports @@
+stringr
@@ Property / imports: stringr / rank @@
+Normal rank
@@ Property / imports @@
+lifecycle
@@ Property / imports: lifecycle / rank @@
+Normal rank
@@ Property / cites work @@
+Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation
+Normal rank
@@ Property / MaRDI profile type @@
+MaRDI software profile
@@ Property / MaRDI profile type: MaRDI software profile / rank @@
+Normal rank
@@ links / mardi / name / links / mardi / name @@
+Software:80333

Latest revision as of 18:55, 12 March 2024

Simulate DNA Alignments Using Node Substitutions

Language	Label	Description	Also known as
English	nodeSub	Simulate DNA Alignments Using Node Substitutions

Statements

instance of

R package

0 references

software version identifier

1.2.5

publication date

19 August 2022

0 references

1.2.2

publication date

11 January 2022

0 references

1.2.3

publication date

1 February 2022

0 references

1.2.4

publication date

24 May 2022

0 references

1.2.7

publication date

15 September 2023

0 references

1.2

publication date

30 September 2021

0 references

1.2.8

publication date

14 November 2023

0 references

0 references

0 references

14 November 2023

0 references

description

Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.

0 references

author

Thijs Janzen

0 references

copyright license

GNU General Public License, version 3.0

0 references

depends on software

Rcpp

0 references

ape

0 references