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PAUP* specifications


Unique identifier OMICS_04239
Name PAUP*
Alternative names Phylogenetic analysis using parsimony*, PAUP
Software type Application/Script
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 4.0
Stability Stable
Maintained No


No version available



This tool is not maintained anymore.

PAUP* citations


Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data

PMCID: 5958176
PMID: 29780268
DOI: 10.3897/zookeys.757.24453
call_split See protocol

[…] des Corp.), complementary strands were aligned, and COI was inspected for proper translation, alignments were done using the MUSCLE option in Sequencher. Neighbor-joining (NJ) trees were generated in PAUP* v4.0b10 (Swofford, 2002) for the 16S and COI data separately, and of the combined data. Scale bars at bottom of each tree represent uncorrected p-distances. […]


Valine glutamine (VQ) motif coding genes are ancient and non plant specific with comprehensive expression regulation by various biotic and abiotic stresses

BMC Genomics
PMCID: 5941492
PMID: 29743038
DOI: 10.1186/s12864-018-4733-7

[…] he Clustal X2 program ( The aligned VQ motif sequences, which were listed in Additional file , were employed for phylogenetic tree construction using the program Mac PAUP 4.0b10 (ppc) ( by both Maximum parsimony (MP) and maximum-likelihood (ML) analyses. Bootstrap supports of specific nodes were estimated with 1000 replicates with […]


Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species

PLoS One
PMCID: 5931476
PMID: 29718922
DOI: 10.1371/journal.pone.0194877
call_split See protocol

[…] and the remainder summarized as a maximum clade credibility tree. Trees were visualised using the APE package []. Strict and semi-strict consensus trees combining the two analyses were constructed in PAUP []. […]


New taxonomic and conservation status of Ossiculum (Vandeae, Orchidaceae), a highly threatened and narrow endemic angraecoid orchid from Central Africa

PMCID: 5943395
PMID: 29750073
DOI: 10.3897/phytokeys.98.23511
call_split See protocol

[…] enic spacer) and 555 accessions representing 316 species from 43 genera (see ). We performed the parsimony and the Bayesian analyses on the combined matrix using, respectively, the computer programme PAUP* v.4.0 a 146 () and MrBayes 3.2.5 (; ).Using the IUCN Red List Categories and Criteria (), we made a preliminary risk of extinction assessment for the species. We imported georeferenced specimen […]


Ginkgo biloba’s footprint of dynamic Pleistocene history dates back only 390,000 years ago

BMC Genomics
PMCID: 5921299
PMID: 29703145
DOI: 10.1186/s12864-018-4673-2

[…] he Inverted Repeat (IR) region and indels. A total of 135 polymorphic sites were identified, of which 15 were parsimony uninformative. Consistency index (CI) and retention index (RI) as calculated by PAUP [] were 95.1% and 99.4%, respectively (CI 93.7% and RI 99.1% calculated without autapomorphies). Network reconstruction revealed 17 individual haplotypes clustered into eight groups (A-H) (Fig. ) […]


BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics

PLoS One
PMCID: 5919079
PMID: 29694383
DOI: 10.1371/journal.pone.0193525

[…] Bank sequences from different geographical regions were utilized for the analysis. A total of 307 unique sequences (including study sequences) of group B RSV focusing on the BA9 lineage were used (). PAUP 4.0 was used for inferring the phylogenetic tree [] and Modeltest3.7 program to estimate the nucleotide substitution rate []. The best model, favoured by Bay’s factor was calculated by path sampl […]


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