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+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
+.TH NTTHAL "1" "December 2013" "2.3.6" "Primer3 User Manuals"
+ntthal \- Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach
+\fBntthal\fR is analogous to \fBntdpal\fR. Between two sequences, \fBntthal\fR finds
+alignment/sec structure, that has the highest melting
+temperature. Ntthal is based on nearest-neighbor thermodynamical
+.B ntthal
+\fIOPTIONS\fR oligo
+\fB\-mv\fR monovalent_conc \- concentration of monovalent cations in mM, by default 50 mM
+\fB\-dv\fR divalent_conc \- concentration of divalent cations in mM, by default 0 mM
+\fB\-n\fR dNTP_conc \- concentration of deoxynycleotide triphosphate in mM, by default 0 mM
+\fB\-d\fR dna_conc \- concentration of DNA strands in nM, by default 50 nM
+\fB\-a\fR mode \- alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)
+\fB\-t\fR temp \- temperature at which duplex is calculated, by default 37C
+\fB\-r\fR \- causes the alignment NOT to be displayed on stderr, _only_ Tm is printed
+\fB\-maxloop\fR size \- the maximum size of secondary structures loops.
+Default is 30 (this is maximum allowed length, currently).
+\fB\-path\fR <path> \- the path to the thermodynamic parameter files
+\fB\-s1\fR DNA_oligomer
+\fB\-s2\fR DNA_oligomer
+This manual page was created by Andreas Tille <> using help2man
+for Debian but can be freely used for any other purpose