Fix a bug

Fix a bug related to estimate confident intervals when having internal date constraints

not precise input dates & unique solution

• sometimes when all tips dates are equal, and there's not any precise input internal dates, we can still have a unique solution. This version explores that possibility and gives back you either the unique solution, or the interval of multiple solutions.
• remove the nexus tree that has branch length as number of substitutions per site from output trees.

fix a bug

fix a bug of integrating internal constraints when rerooting

fix some bugs

• remove limit on number of iterations for active set method
• fix bug missing label on null branches nodes

fix some bugs

• fix some bugs about inconsistent date formats, invalid CI values on collapsed branches, collapsed branches with unrooted tree
• output root to tip distances and dates when using verbose mode (-j)

use bootstrap trees for confidence intervals, fix some bugs

• Allow to use bootstrap trees to calculate confidence intervals of rates and dates, use the same option -f. So -f can be either the number of sampling simulation or a file containing bootstrap trees.
• Fix some bugs related to unrooted trees and outgroups.

fix some bugs, change default setting

• set temporal constraint and using variances by default (so now don't need to use -c and -v 1)
• fix bugs missing internal nodes label (or support) in output tree in some cases (rooting the tree)
• fix bugs setting minblen=-1 when estimating relative dates
• allow mix of date formats among year-month-day, year-month and year
• allow to not collapse any branch by setting a negative value for -l
• improve nexus format to be able to read in R

collapse branches, minimum branches length, date format year-month-day, lsd2 as library

• collapse uninformative branches before analysis (branch length <= 0.5/seqlength by default, settable via option -l ; or low support value if available, settable via option -S).
• impose minimum branch length for time scaled tree (estimate by default, settable via option -u for internal branches and -U for external branches). By default this minimum branch length is rounded to number of days with rounding factor 365 (settable via option -R).
• in addition to real number, date can also have format year-month-date. The output date format is decided based on the input date format, but can set via option -D.
• LSD2 is included as a library in IQ-tree (thanks @bqminh ).

new setting for variances and confidence intervals

• The parameter used to adjust variances (-b) is set as the unit of branch lengths (instead of percent as before). The default value is the median of branch lengths.
• Allow to apply a lognormal relaxed clock on branch lengths when calculating confidence intervals. The standard deviation is set by option -q, and default is 0.2. Actual sequence length is required and used to simulate branch lengths.

fix bugs for internal nodes outliers

v1.4.2.2

update version