my first authorship paper from my PhD was changed at last minute to a co-authorship... is it gonna affect in any way my career? I recently finished my PhD in Developmental Biology in the US, but I left a couple of experiments completed prior to finishing the paper. (This paper was developed during the course of my PhD and has had numerous changes).

I have since finished my PhD and my supervisor started to take my paper and made decisions on it. He never once asked me for my Drosophila collection, and we never ever discussed the paper and how we could finish it.  I became depressed as he treated like I am stupid, even though the paper was almost done and it was worthy of a high-impact journal... He never seemed to trust in my capabilities. 

I have since realised that he found a new grad student to finish those experiments (that I could perfectly have done faster and in a much shorter time)... and now (almost a year later) my paper was submitted. Unfortunately, he decided to make the other PhD student the second first co-author of my paper. 

I would like to hear some opinions as I don't know what to do. 
Is this going to impact my future career? 
I also don't understand how someone that knows deep inside that I am the first author of a paper can do this?
The title and body-text of your question do not match. The former describes the change of authorship as "last minute" whilst the latter says that the paper was developed from your drafts "almost a year later".

Also, could you clarify what you mean by "second first co-author"? Is that a euphemism for "second author"?

Anyhow, there is a big difference between:


a complete paper having the authorship order changed unilaterally by the corresponding author at the time of submission (which is what "last minute" would imply); and
a draft paper being developed and completed by a new co-author, who is then given precedence over the person who wrote the original draft (which is what the body of your question implies).


If §1 applies, then the person who acted unilaterally acted improperly (even if the authorship order does warrant change, the change should be done transparently).

If §2 applies, then, based on the information available, the situation amounts to a dispute rather than to misconduct. In some circumstances, it may be perfectly reasonable for a person who turned a draft into a complete paper worthy of publication to take precedence over the person who wrote the draft originally. Without knowing the details of the case, it is difficult to say who is in the right.

Your options:


A) complain to the editor/publisher (be prepared to provide detailed evidence to substantiate your argument, such as the drafts with their original timestamps) -- possible outcomes include nothing happening (if the editor/publisher disagrees with your claims), change of authorship order, addition or removal of co-authors, or retraction of the paper;
B) (may require you to have attempted §C already) complain to the university's research conduct office or equivalent (as with §A, be prepared to provide detailed evidence) -- possible outcomes as per §A, plus possibility of disciplinary action if the university considers serious misconduct to have taken place;
C) complain to the corresponding author (you may want suggest that it was oversight rather than out of malice... it is possible that, with the distance of time, your contribution was forgotten unintentionally) -- possible outcomes as per §A, although if any changes are made to the author list, the corresponding author will then have to convince the editor/publisher that the changes should be made (editors do not permit changes without justification, in order to prevent "gift authorship");
D) engage legal counsel and complain through the courts: IANAL, but a likely argument would be that your moral rights (specifically, the "right of paternity": that is, to be recognised as the creator of a work) were not recognised properly (if, moreover, you have not assigned copyright to the university, you may be able to sue for copyright infringement).