CONSEL: for assessing the confidence of phylogenetic tree selection

By Hidetoshi Shimodaira, Masami Hasegawa. Bioinform., 2001

2,098 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9b872e84d8f7ae03cdcb3c47d7db2f625dbec64b

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Citations in the corpus

The phylogeny and limits of Elateridae (Insecta, Coleoptera): is there a common tendency of click beetles to soft‐bodiedness and neoteny? (2011, methodology): “Considering available information on the molecular phylogeny of Elateridae and high similarity of these results with the morphology-based approach published by Johnson (2002), we propose the following modifications of the elaterid classification published by Costa et al. (2010).”
Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences (2006, methodology): “…tests were used to evaluate a set of alternative phylogenetic trees obtained by constraining the topologies of interest using the appropriate options in paup*. AU and SH tests were carried out using consel version 0.1f (Shimodaira & Hasegawa, 2001) with site likelihoods calculated using paup*.”
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2019, methodology): “For the AA-data set, CONSEL took 9.4 min and IQ-TREE 2 took 8.7 min with one CPU core and 2.4 min with four CPU cores.”
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments (2010, background): “On the larger alignments, RAxML 7.2.1’s likelihoods were much higher than FastTree’s, and all of the differences in likelihood were statistically significant (all P~0, SH test using CONSEL [28]).”
Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography (2009, methodology): “…placement of Bothriechis lateralis as the sister lineage to Bothriechis bicolor (Crother et al., 1992) using the Shimodaira–Hasegawa (SH) test (Shimodaira & Hasegawa, 1999) and the approximately unbiased (AU) test (Shimodaira, 2002) implemented in the program consel (Shimodaira & Hasegawa, 2001).”
Pvclust: an R package for assessing the uncertainty in hierarchical clustering (2006, methodology): “The multiscale bootstrap resampling was developed recently (Efron et al., 1996; Shimodaira, 2002, 2004) for calculating approximately unbiased (AU) probability values (p-values) as implemented in a software CONSEL (Shimodaira and Hasegawa, 2001).”
New insights into the phylogeny, systematics and DNA barcoding of Nemertea (2014, methodology): “Per site log-likelihood values (which summed constitute the log-likelihood of a phylogram) were calculated in RAxML using the ‘-f g’ option (RAxML was called as follows: raxmlHPC-HYBRID -T 6 -s input_file –n results -p 12345 -m GTRGAMMA -f g -z best_constrained_tree) and these were subsequently subm”
INTER‐ AND INTRASPECIFIC VARIATION OF THE PSEUDO‐NITZSCHIA DELICATISSIMA COMPLEX (BACILLARIOPHYCEAE) ILLUSTRATED BY RRNA PROBES, MORPHOLOGICAL DATA AND PHYLOGENETIC ANALYSES 1 (2006, methodology): “To compare several user-defined trees versus the optimal tree obtained by ML analysis, the approximately unbiased test (AU test) was performed using Consel 1.0f (Shimodaira and Hasegawa 2001) (Table 3).”