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TN93 specifications

Information


Unique identifier OMICS_25048
Name TN93
Alternative name Tamura Nei 93
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.0.4
Stability Stable
Requirements
GCC, Cmake
Maintained Yes

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TN93 citations

 (27)
library_books

HIV 1 genetic transmission networks among men who have sex with men in Kunming, China

2018
PLoS One
PMCID: 5919538
PMID: 29698467
DOI: 10.1371/journal.pone.0196548

[…] ity) and low intra-cluster genetic distance. The phylogenetic tree was constructed with 308 MSM pol sequences identified in Kunming during 2010–2015, by using the neighbor-joining method based on the Tamura-Nei 93 model (). The transmission clusters were extracted from the phylogenetic tree using Cluster Picker software []. Transmission clusters were defined as those with node support thresholds g […]

call_split

Emerging Coxsackievirus A6 Causing Hand, Foot and Mouth Disease, Vietnam

2018
PMCID: 5875260
PMID: 29553326
DOI: 10.3201/eid2404.171298
call_split See protocol

[…] or viral capsid protein 1 (VP1) and complete coding sequences (CDS) using IQ-TREE version 1.4.3 (). The maximum likelihood phylogenetic analysis used the general time reversible (for CDS dataset) and Tamura-Nei 93 (for VP1 dataset) nucleotide substitution models with a gamma distributed among site rate variation (4 rate categories). We assessed support for individual nodes using a bootstrap proced […]

call_split

Multiplex PCR−Based Next Generation Sequencing and Global Diversity of Seoul Virus in Humans and Rats

2018
PMCID: 5782898
PMID: 29350137
DOI: 10.3201/eid2402.171216
call_split See protocol

[…] y and high throughput algorithm (). We generated phylogenetic trees by using the maximum-likelihood method in MEGA version 6.0 () and models for analysis according to the best fit substitution model (TN93 + gamma + invariate for L segments, general time reversible + gamma + invariant for M segments, and T92 + gamma for S segments). We assessed support for topologies by bootstrapping for 1,000 iter […]

library_books

Examination of Sarcocystis spp. of giant snakes from Australia and Southeast Asia confirms presence of a known pathogen – Sarcocystis nesbitti

2017
PLoS One
PMCID: 5683627
PMID: 29131856
DOI: 10.1371/journal.pone.0187984

[…] ing the Maximum Composite Likelihood method with Gamma-distributed substitutions (G) and variation among lineages (as observed for the coccidia; []) under the Minimum Evolution (ME) algorithm, or the Tamura-Nei-93 model with G and invariant sites (I) under the Maximum Likelihood (ML) algorithm. Substitution rate variation among sites was estimated by ML over five Gamma categories and the number of […]

call_split

Characteristics of HIV infected U.S. Army soldiers linked in molecular transmission clusters, 2001 2012

2017
PLoS One
PMCID: 5536263
PMID: 28759645
DOI: 10.1371/journal.pone.0182376
call_split See protocol

[…] s that were highly related to each other (i.e. a cluster). The cutoff value was established by identifying an optimal intra-cluster genetic distance using available sequences for all Soldiers (). The Tamura-Nei 93 distance model was used as well to confirm sequence relatedness and showed no significant differences from the K2P model (). Transmitted drug resistance mutations were identified using t […]

call_split

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

2017
Nat Commun
PMCID: 5500885
PMID: 28675384
DOI: 10.1038/ncomms16046
call_split See protocol

[…] We then removed from the alignment all columns where at least one mtDNA presented a gap or missing data, resulting in 15,345 positions. We run Modelgenerator v.85 (ref. ) on our data set to identify Tamura-Nei 93 with a fixed fraction of invariable sites as the best-supported model. We set a fixed mutation rate (1.57 × 10−8 μ site−1 year−1) calculated for the coding region of modern humans with a […]

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