diff --git a/src/Cargo.lock b/src/Cargo.lock index d3a61d54..9bf84ff4 100644 --- a/src/Cargo.lock +++ b/src/Cargo.lock @@ -1793,7 +1793,7 @@ dependencies = [ [[package]] name = "obikmer" -version = "1.1.44" +version = "1.2.0" dependencies = [ "clap", "csv", diff --git a/src/obikmer/Cargo.toml b/src/obikmer/Cargo.toml index 903c69db..34b4c9e3 100644 --- a/src/obikmer/Cargo.toml +++ b/src/obikmer/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "obikmer" -version = "1.1.44" +version = "1.2.0" edition = "2024" [[bin]] diff --git a/src/obikmer/src/cmd/phylo/tnt.rs b/src/obikmer/src/cmd/phylo/tnt.rs index c3c13a08..334a8f16 100644 --- a/src/obikmer/src/cmd/phylo/tnt.rs +++ b/src/obikmer/src/cmd/phylo/tnt.rs @@ -46,6 +46,10 @@ pub(super) fn write_sankoff_tnt( let n_sites = alignment.sequences.first().map(|s| s.len()).unwrap_or(0); writeln!(f, "xread").unwrap(); + writeln!(f, "mxram 16000;").unwrap(); + writeln!(f, "taxname =;").unwrap(); + writeln!(f, "taxname +50;").unwrap(); + writeln!( f, "'obikmer central-position SNP families, calibrated Sankoff 16-state encoding'" @@ -166,9 +170,7 @@ pub(super) fn write_sankoff_tnt( writeln!(f, ";").unwrap(); writeln!(f, "hold 20;").unwrap(); writeln!(f, "mult;").unwrap(); - writeln!(f, "taxname =;").unwrap(); - writeln!(f, "tsave * {tre_name};").unwrap(); - writeln!(f, "tsave /;").unwrap(); + writeln!(f, "export - {tre_name};").unwrap(); info!( "TNT script → {path} (costs scaled x{cost_scale:.0}, runs a default `hold 20; mult;` \