CONSEL is a program designed to assess the confidence of phylogenetic tree selection by calculating p-values for various tests, including the Bootstrap Probability (BP), Kishino–Hasegawa (KH) test, Shimodaira–Hasegawa (SH) test, Weighted Shimodaira–Hasegawa (WSH) test, and the Approximately Unbiased (AU) test. The program uses the multi-scale bootstrap technique to calculate the p-value of the AU test, which is less biased than other conventional p-values. CONSEL can handle a wide range of problems where Bootstrap Probabilities (BPs) are available, and it is applicable to phylogeny programs like Molphy, PAML, and PAUP*. The program consists of two parts: makermt, which reads the matrix of site-wise log-likelihoods and generates bootstrap replicates, and consel, which calculates the p-values for the candidate trees. The AU test, developed to reduce bias, is based on the smoothness of hypothesis region boundaries and is accurate for most cases. CONSEL accepts three types of input files for the AU test: rmt, rep, and cnt, making it versatile for various selection criteria and hypothesis tests.CONSEL is a program designed to assess the confidence of phylogenetic tree selection by calculating p-values for various tests, including the Bootstrap Probability (BP), Kishino–Hasegawa (KH) test, Shimodaira–Hasegawa (SH) test, Weighted Shimodaira–Hasegawa (WSH) test, and the Approximately Unbiased (AU) test. The program uses the multi-scale bootstrap technique to calculate the p-value of the AU test, which is less biased than other conventional p-values. CONSEL can handle a wide range of problems where Bootstrap Probabilities (BPs) are available, and it is applicable to phylogeny programs like Molphy, PAML, and PAUP*. The program consists of two parts: makermt, which reads the matrix of site-wise log-likelihoods and generates bootstrap replicates, and consel, which calculates the p-values for the candidate trees. The AU test, developed to reduce bias, is based on the smoothness of hypothesis region boundaries and is accurate for most cases. CONSEL accepts three types of input files for the AU test: rmt, rep, and cnt, making it versatile for various selection criteria and hypothesis tests.