├── .github └── workflows │ └── build.yml ├── LICENSE ├── Makefile ├── README.md ├── RelativeNMI_species.png ├── WFA2 ├── Makefile ├── affine2p_penalties.h ├── affine_penalties.h ├── bitmap.c ├── bitmap.h ├── cigar.c ├── cigar.h ├── commons.h ├── heatmap.c ├── heatmap.h ├── linear_penalties.h ├── mm_allocator.c ├── mm_allocator.h ├── mm_stack.h ├── profiler_counter.c ├── profiler_counter.h ├── profiler_timer.c ├── profiler_timer.h ├── score_matrix.h ├── string_padded.c ├── string_padded.h ├── vector.c ├── vector.h ├── wavefront.c ├── wavefront.h ├── wavefront_align.c ├── wavefront_align.h ├── wavefront_aligner.c ├── wavefront_aligner.h ├── wavefront_attributes.c ├── wavefront_attributes.h ├── wavefront_backtrace.c ├── wavefront_backtrace.h ├── wavefront_backtrace_buffer.c ├── wavefront_backtrace_buffer.h ├── wavefront_backtrace_offload.c ├── wavefront_backtrace_offload.h ├── wavefront_bialign.c ├── wavefront_bialign.h ├── wavefront_bialigner.c ├── wavefront_bialigner.h ├── wavefront_components.c ├── wavefront_components.h ├── wavefront_compute.c ├── wavefront_compute.h ├── wavefront_compute_affine.c ├── wavefront_compute_affine.h ├── wavefront_compute_affine2p.c ├── wavefront_compute_affine2p.h ├── wavefront_compute_edit.c ├── wavefront_compute_edit.h ├── wavefront_compute_linear.c ├── wavefront_compute_linear.h ├── wavefront_debug.c ├── wavefront_debug.h ├── wavefront_display.h ├── wavefront_extend.c ├── wavefront_extend.h ├── wavefront_heuristic.c ├── wavefront_heuristic.h ├── wavefront_offset.h ├── wavefront_pcigar.c ├── wavefront_pcigar.h ├── wavefront_penalties.c ├── wavefront_penalties.h ├── wavefront_plot.c ├── wavefront_plot.h ├── wavefront_slab.c ├── wavefront_slab.h ├── wavefront_unialign.c └── wavefront_unialign.h ├── alignment.c ├── alignment.h ├── alignment_macros.h ├── alignment_scoring.c ├── alignment_scoring.h ├── ancestralclust ├── ancestralclust.c ├── cluster_ancestral.png ├── global.h ├── hashmap.c ├── hashmap.h ├── kalign ├── align_io.h ├── alignment_parameters.c ├── alignment_parameters.h ├── aln_controller.c ├── aln_controller.h ├── aln_mem.c ├── aln_mem.h ├── aln_profileprofile.c ├── aln_profileprofile.h ├── aln_run.c ├── aln_run.h ├── aln_seqprofile.c ├── aln_seqprofile.h ├── aln_seqseq.c ├── aln_seqseq.h ├── aln_setup.c ├── aln_setup.h ├── aln_struct.h ├── aln_task.c ├── aln_task.h ├── alphabet.c ├── alphabet.h ├── bisectingKmeans.c ├── bisectingKmeans.h ├── bpm.h ├── config.h ├── esl_stopwatch.c ├── esl_stopwatch.h ├── euclidean_dist.c ├── euclidean_dist.h ├── global.h ├── idata.c ├── idata.h ├── misc.h ├── msa.h ├── parameters.c ├── parameters.h ├── pick_anchor.c ├── pick_anchor.h ├── run_kalign.c ├── rwalign.c ├── sequence_distance.c ├── sequence_distance.h ├── tldevel.c ├── tldevel.h ├── tlmisc.c ├── tlmisc.h ├── tlrng.c ├── tlrng.h ├── weave_alignment.c └── weave_alignment.h ├── lran2.h ├── malloc-2.8.3.h ├── math.c ├── math.h ├── needleman_wunsch.c ├── needleman_wunsch.h ├── opt.c ├── opt.h ├── 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