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TFPGA specifications

Information


Unique identifier OMICS_29893
Name TFPGA
Alternative name Tools For Population Genetic Analyses
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mark Miller

TFPGA citations

 (93)
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Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation

2018
Sci Rep
PMCID: 5915404
PMID: 29691494
DOI: 10.1038/s41598-018-24912-z
call_split See protocol

[…] a vs. Korea”, “China vs. Japan”, and “Korea vs. Japan”).We conducted unweighted pair-group method with arithmetic means (UPGMA) based on Nei’s unbiased genetic distances between populations using the Tfpga 1.3 program. Bootstrap values for nodes were estimated based on 999 replications. As a complementary analysis, we performed a principal coordinate analysis (PCoA) with GenAlEx, on the basis of N […]

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Life histories and ecotype conservation in an adaptive vertebrate: Genetic constitution of piscivorous brown trout covaries with habitat stability

2018
Ecol Evol
PMCID: 5838037
PMID: 29531690
DOI: 10.1002/ece3.3828
call_split See protocol

[…] iteria. Tests for null alleles, large allele dropouts, and scoring errors were performed in MICRO‐CHECKER v.2.2.3 after 10,000 iterations (Van Oosterhout, Hutchinson, Wills, & Shipley, ). The program TFPGA v.1.3 (Miller, ) was used for descriptive statistics (number of alleles, observed, and expected heterozygosity [H o and H e]). Allelic richness (A r) among samples was estimated in FSTAT v.2.9.3 […]

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Historical isolation and contemporary gene flow drive population diversity of the brown alga Sargassum thunbergii along the coast of China

2017
BMC Evol Biol
PMCID: 5721624
PMID: 29216823
DOI: 10.1186/s12862-017-1089-6
call_split See protocol

[…] To visualize the phylogenetic relationships among samples, an unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance [] was constructed using the program TFPGA []. Bootstrap analysis (1000 pseudoreplicates) was used to evaluate statistical nodal support. […]

library_books

Isolation and characterization of 30 microsatellite loci for Cunninghamia lanceolata (Taxodiaceae)1

2017
Appl Plant Sci
PMCID: 5628030
PMID: 28989826
DOI: 10.3732/apps.1700060

[…] rom three to 30 with an average of 9.4 using FSTAT 2.9.3 software () (). The observed and expected heterozygosities ranged from 0.0313–0.8333 and 0.0313–0.9246, respectively, analyzed by the software TFPGA version 1.3 () (). After the sequential Bonferroni adjustment (), only two loci (CL34 and CL723) displayed significant deviations from Hardy–Weinberg equilibrium (P < 0.05) in all three populati […]

library_books

De Novo Assembly of Transcriptome and Development of Novel EST SSR Markers in Rhododendron rex Lévl. through Illumina Sequencing

2017
Front Plant Sci
PMCID: 5622969
PMID: 29018469
DOI: 10.3389/fpls.2017.01664

[…] _CALC version 0.6 (Botstein et al., ). Hardy-Weinberg equilibrium (HWE) for each locus was calculated by Genepop version 4.1.4 (Yeh et al., ). The unweighted pair group mean analysis was estimated by TFPGA version 1.3 (Miller, ) with 5,000 permutations. Principal coordinates analysis (PCA) was visualized R software by ape package (Paradis et al., ). […]

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Genetic diversity, population structure, and traditional culture of Camellia reticulata

2017
Ecol Evol
PMCID: 5677478
PMID: 29152187
DOI: 10.1002/ece3.3340
call_split See protocol

[…] & Excoffier, ) and analyzed from both among populations and within populations. The UPGMA dendrogram of populations based on AFLP fingerprints was drawn based on pairwise similarities using software TFPGA (Miller, ).To further elucidate relationships among all populations, a model‐based cluster analysis was performed using the program STRUCTURE v2.3.1 (Raj, Stephens, & Pritchard, ). STRUCTURE was […]

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